wishlist for readGappedAlignments
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Tengfei Yin ▴ 420
@tengfei-yin-4323
Last seen 8.6 years ago
Dear all, I am using GenomicRanges and Rsamtools a lot for my work, they are extremely helpful and neat packages to deal with NGS data, thanks a lot for those people how contribute to all those nice packages in BioC. I just have some features request for the GappedAlignments, probably it's already there or it's not a good practice to do it in certain way, please feel free to let me know. I like features from both scanBam or readBamGappedAlignments, just sometime I need to write my own script trying to combine information from those two function and make a "general" granges to work with. So I am wondering if there is any way to do it in a neat way or is there a plan to implement similiar features? - Including more element meta data with GappedAlignments - there is "which" in readBamGappedAlignments, can I have some thing like "param" or "what" to get more info from bam file and associate them with Gapped reads. - When doing the coerce from GappedAlignement to GRanges, or call granges() on GappedAlignments object, it only return the minimal information, "qwidth", "cigar", "ngap" is not included as elementMetadata. - Including more pairing information for pair-end RNA-seq - So I could know the mated information with certain gapped reads, either plot it as pair-end read or do some computation on it. - Setting flags for each entry, so I can filter it out based on the flags, something like from scanBamFlag? - grglist to transform the data in different way If I can get a general data structure which combine all those information and or features together, that would be nice, I realize it's hard to combine all information together and make it flexible at the same time , e.g. you need to deal with how to binding element meta data for paired entry, probably showing seq1/seq2 to indicate which sequence it's belongs too? how to handle multiple hits? Right now, I am making my own "giant" GRanges object which including all the information I want, but that's too specific for my work, that's why I am wondering if there is any plan to combine those neat features together and bring a more flexible data structure. Thanks! Tengfei -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]]
GenomicRanges Rsamtools GenomicRanges Rsamtools • 1.4k views
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Cory Barr ▴ 60
@cory-barr-4429
Last seen 10.2 years ago
I would find being able to pass the "what" component of a ScanBamParam object to readBamGappedAlignments very helpful. Like Tengfei, I often read in a BAM file from readBamGappedAlignments and also scanBam then combine the information. Being able to maintain information on a read's mate via readBamGappedAlignments would also get much use from me. Currently, to do this I combine information from scanBam, parse out the end number from the BAM flag, and then regroup a GRangesList to include its mate. Doing this efficiently by passing an argument to grglist would be great. -Cory On Tue, Aug 9, 2011 at 11:33 AM, Tengfei Yin <yintengfei@gmail.com> wrote: > Dear all, > > I am using GenomicRanges and Rsamtools a lot for my work, they are > extremely > helpful and neat packages to deal with NGS data, thanks a lot for those > people how contribute to all those nice packages in BioC. I just have some > features request for the GappedAlignments, probably it's already there or > it's not a good practice to do it in certain way, please feel free to let > me > know. > > I like features from both scanBam or readBamGappedAlignments, just > sometime > I need to write my own script trying to combine information from those two > function and make a "general" granges to work with. So I am wondering if > there is any way to do it in a neat way or is there a plan to implement > similiar features? > > - Including more element meta data with GappedAlignments > - there is "which" in readBamGappedAlignments, can I have some thing > like "param" or "what" to get more info from bam file and associate > them > with Gapped reads. > - When doing the coerce from GappedAlignement to GRanges, or call > granges() on GappedAlignments object, it only return the minimal > information, "qwidth", "cigar", "ngap" is not included as > elementMetadata. > - Including more pairing information for pair-end RNA-seq > - So I could know the mated information with certain gapped reads, > either plot it as pair-end read or do some computation on it. > - Setting flags for each entry, so I can filter it out based on the > flags, something like from scanBamFlag? > - grglist to transform the data in different way > > If I can get a general data structure which combine all those information > and or features together, that would be nice, I realize it's hard to > combine all information together and make it flexible at the same time , > e.g. you need to deal with how to binding element meta data for paired > entry, probably showing seq1/seq2 to indicate which sequence it's belongs > too? how to handle multiple hits? > > Right now, I am making my own "giant" GRanges object which including all > the > information I want, but that's too specific for my work, that's why I am > wondering if there is any plan to combine those neat features together and > bring a more flexible data structure. > > Thanks! > > Tengfei > > > -- > Tengfei Yin > MCDB PhD student > 1620 Howe Hall, 2274, > Iowa State University > Ames, IA,50011-2274 > Homepage: www.tengfei.name > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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On 08/09/2011 11:58 AM, Cory Barr wrote: > I would find being able to pass the "what" component of a ScanBamParam > object to readBamGappedAlignments very helpful. Like Tengfei, I often read > in a BAM file from readBamGappedAlignments and also scanBam then combine the > information. As a start, GappedAlignments() in 1.5.23 has a new ... argument used to populate elementMetadata. So e.g., bam <- scanBam(<...>) with(bam[[1]], GappedAlignments(<...>, qual=qual)) Martin > Being able to maintain information on a read's mate via > readBamGappedAlignments would also get much use from me. Currently, to do > this I combine information from scanBam, parse out the end number from the > BAM flag, and then regroup a GRangesList to include its mate. Doing this > efficiently by passing an argument to grglist would be great. > > -Cory > > On Tue, Aug 9, 2011 at 11:33 AM, Tengfei Yin<yintengfei at="" gmail.com=""> wrote: > >> Dear all, >> >> I am using GenomicRanges and Rsamtools a lot for my work, they are >> extremely >> helpful and neat packages to deal with NGS data, thanks a lot for those >> people how contribute to all those nice packages in BioC. I just have some >> features request for the GappedAlignments, probably it's already there or >> it's not a good practice to do it in certain way, please feel free to let >> me >> know. >> >> I like features from both scanBam or readBamGappedAlignments, just >> sometime >> I need to write my own script trying to combine information from those two >> function and make a "general" granges to work with. So I am wondering if >> there is any way to do it in a neat way or is there a plan to implement >> similiar features? >> >> - Including more element meta data with GappedAlignments >> - there is "which" in readBamGappedAlignments, can I have some thing >> like "param" or "what" to get more info from bam file and associate >> them >> with Gapped reads. >> - When doing the coerce from GappedAlignement to GRanges, or call >> granges() on GappedAlignments object, it only return the minimal >> information, "qwidth", "cigar", "ngap" is not included as >> elementMetadata. >> - Including more pairing information for pair-end RNA-seq >> - So I could know the mated information with certain gapped reads, >> either plot it as pair-end read or do some computation on it. >> - Setting flags for each entry, so I can filter it out based on the >> flags, something like from scanBamFlag? >> - grglist to transform the data in different way >> >> If I can get a general data structure which combine all those information >> and or features together, that would be nice, I realize it's hard to >> combine all information together and make it flexible at the same time , >> e.g. you need to deal with how to binding element meta data for paired >> entry, probably showing seq1/seq2 to indicate which sequence it's belongs >> too? how to handle multiple hits? >> >> Right now, I am making my own "giant" GRanges object which including all >> the >> information I want, but that's too specific for my work, that's why I am >> wondering if there is any plan to combine those neat features together and >> bring a more flexible data structure. >> >> Thanks! >> >> Tengfei >> >> >> -- >> Tengfei Yin >> MCDB PhD student >> 1620 Howe Hall, 2274, >> Iowa State University >> Ames, IA,50011-2274 >> Homepage: www.tengfei.name >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Thanks Tengfei and Cory for the feedback. Those requests make a lot of sense and we agree that the GappedAlignments container will benefit a lot from this kind of improvements. We'll do our best to implement most of them in one way or another before the next release. Cheers, H. On 11-08-09 01:50 PM, Martin Morgan wrote: > On 08/09/2011 11:58 AM, Cory Barr wrote: >> I would find being able to pass the "what" component of a ScanBamParam >> object to readBamGappedAlignments very helpful. Like Tengfei, I often >> read >> in a BAM file from readBamGappedAlignments and also scanBam then >> combine the >> information. > > As a start, GappedAlignments() in 1.5.23 has a new ... argument used to > populate elementMetadata. So e.g., > > bam <- scanBam(<...>) > with(bam[[1]], GappedAlignments(<...>, qual=qual)) > > Martin > >> Being able to maintain information on a read's mate via >> readBamGappedAlignments would also get much use from me. Currently, to do >> this I combine information from scanBam, parse out the end number from >> the >> BAM flag, and then regroup a GRangesList to include its mate. Doing this >> efficiently by passing an argument to grglist would be great. >> >> -Cory >> >> On Tue, Aug 9, 2011 at 11:33 AM, Tengfei Yin<yintengfei at="" gmail.com=""> wrote: >> >>> Dear all, >>> >>> I am using GenomicRanges and Rsamtools a lot for my work, they are >>> extremely >>> helpful and neat packages to deal with NGS data, thanks a lot for those >>> people how contribute to all those nice packages in BioC. I just have >>> some >>> features request for the GappedAlignments, probably it's already >>> there or >>> it's not a good practice to do it in certain way, please feel free to >>> let >>> me >>> know. >>> >>> I like features from both scanBam or readBamGappedAlignments, just >>> sometime >>> I need to write my own script trying to combine information from >>> those two >>> function and make a "general" granges to work with. So I am wondering if >>> there is any way to do it in a neat way or is there a plan to implement >>> similiar features? >>> >>> - Including more element meta data with GappedAlignments >>> - there is "which" in readBamGappedAlignments, can I have some thing >>> like "param" or "what" to get more info from bam file and associate >>> them >>> with Gapped reads. >>> - When doing the coerce from GappedAlignement to GRanges, or call >>> granges() on GappedAlignments object, it only return the minimal >>> information, "qwidth", "cigar", "ngap" is not included as >>> elementMetadata. >>> - Including more pairing information for pair-end RNA-seq >>> - So I could know the mated information with certain gapped reads, >>> either plot it as pair-end read or do some computation on it. >>> - Setting flags for each entry, so I can filter it out based on the >>> flags, something like from scanBamFlag? >>> - grglist to transform the data in different way >>> >>> If I can get a general data structure which combine all those >>> information >>> and or features together, that would be nice, I realize it's hard to >>> combine all information together and make it flexible at the same time , >>> e.g. you need to deal with how to binding element meta data for paired >>> entry, probably showing seq1/seq2 to indicate which sequence it's >>> belongs >>> too? how to handle multiple hits? >>> >>> Right now, I am making my own "giant" GRanges object which including all >>> the >>> information I want, but that's too specific for my work, that's why I am >>> wondering if there is any plan to combine those neat features >>> together and >>> bring a more flexible data structure. >>> >>> Thanks! >>> >>> Tengfei >>> >>> >>> -- >>> Tengfei Yin >>> MCDB PhD student >>> 1620 Howe Hall, 2274, >>> Iowa State University >>> Ames, IA,50011-2274 >>> Homepage: www.tengfei.name >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Hi Martin and Hervé , Thank you so much for the updates and response to those requests, I am looking forward to the new features and next release of those packages. Cheers, Tengfei 2011/8/10 Hervé Pagès <hpages@fhcrc.org> > Thanks Tengfei and Cory for the feedback. Those requests make > a lot of sense and we agree that the GappedAlignments container > will benefit a lot from this kind of improvements. We'll do our > best to implement most of them in one way or another before the > next release. > > Cheers, > H. > > > > On 11-08-09 01:50 PM, Martin Morgan wrote: > >> On 08/09/2011 11:58 AM, Cory Barr wrote: >> >>> I would find being able to pass the "what" component of a ScanBamParam >>> object to readBamGappedAlignments very helpful. Like Tengfei, I often >>> read >>> in a BAM file from readBamGappedAlignments and also scanBam then >>> combine the >>> information. >>> >> >> As a start, GappedAlignments() in 1.5.23 has a new ... argument used to >> populate elementMetadata. So e.g., >> >> bam <- scanBam(<...>) >> with(bam[[1]], GappedAlignments(<...>, qual=qual)) >> >> Martin >> >> Being able to maintain information on a read's mate via >>> readBamGappedAlignments would also get much use from me. Currently, to do >>> this I combine information from scanBam, parse out the end number from >>> the >>> BAM flag, and then regroup a GRangesList to include its mate. Doing this >>> efficiently by passing an argument to grglist would be great. >>> >>> -Cory >>> >>> On Tue, Aug 9, 2011 at 11:33 AM, Tengfei Yin<yintengfei@gmail.com> >>> wrote: >>> >>> Dear all, >>>> >>>> I am using GenomicRanges and Rsamtools a lot for my work, they are >>>> extremely >>>> helpful and neat packages to deal with NGS data, thanks a lot for those >>>> people how contribute to all those nice packages in BioC. I just have >>>> some >>>> features request for the GappedAlignments, probably it's already >>>> there or >>>> it's not a good practice to do it in certain way, please feel free to >>>> let >>>> me >>>> know. >>>> >>>> I like features from both scanBam or readBamGappedAlignments, just >>>> sometime >>>> I need to write my own script trying to combine information from >>>> those two >>>> function and make a "general" granges to work with. So I am wondering if >>>> there is any way to do it in a neat way or is there a plan to implement >>>> similiar features? >>>> >>>> - Including more element meta data with GappedAlignments >>>> - there is "which" in readBamGappedAlignments, can I have some thing >>>> like "param" or "what" to get more info from bam file and associate >>>> them >>>> with Gapped reads. >>>> - When doing the coerce from GappedAlignement to GRanges, or call >>>> granges() on GappedAlignments object, it only return the minimal >>>> information, "qwidth", "cigar", "ngap" is not included as >>>> elementMetadata. >>>> - Including more pairing information for pair-end RNA-seq >>>> - So I could know the mated information with certain gapped reads, >>>> either plot it as pair-end read or do some computation on it. >>>> - Setting flags for each entry, so I can filter it out based on the >>>> flags, something like from scanBamFlag? >>>> - grglist to transform the data in different way >>>> >>>> If I can get a general data structure which combine all those >>>> information >>>> and or features together, that would be nice, I realize it's hard to >>>> combine all information together and make it flexible at the same time , >>>> e.g. you need to deal with how to binding element meta data for paired >>>> entry, probably showing seq1/seq2 to indicate which sequence it's >>>> belongs >>>> too? how to handle multiple hits? >>>> >>>> Right now, I am making my own "giant" GRanges object which including all >>>> the >>>> information I want, but that's too specific for my work, that's why I am >>>> wondering if there is any plan to combine those neat features >>>> together and >>>> bring a more flexible data structure. >>>> >>>> Thanks! >>>> >>>> Tengfei >>>> >>>> >>>> -- >>>> Tengfei Yin >>>> MCDB PhD student >>>> 1620 Howe Hall, 2274, >>>> Iowa State University >>>> Ames, IA,50011-2274 >>>> Homepage: www.tengfei.name >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> ______________________________**_________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat="" .ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: >>>> http://news.gmane.org/gmane.**science.biology.informatics.**condu ctor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>> >>>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: >>> http://news.gmane.org/gmane.**science.biology.informatics.**conduc tor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>> >> >> >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]]
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@martin-morgan-1513
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Hi Tengfei -- We've acted on some of your suggestions (e.g., incorporating any field in GappedAlignments, making readBamGappedAlignments accept a ScanBamParam() when Rsamtools 1.5.53 becomes avaiable), thanks! We're really interested in hearing from you and others about specific use cases for paired-end representations, particularly those operations that are difficult to do with the current GappedAlignments (e.g., the distribution of insertion sizes could now be easily extracted as ScanBamParam(what="isize", flag=scanBamFlag(isProperPair=TRUE, isPrimaryRead=TRUE))). So please forward any specific use cases! Martin On 08/09/2011 11:33 AM, Tengfei Yin wrote: > Dear all, > > I am using GenomicRanges and Rsamtools a lot for my work, they are extremely > helpful and neat packages to deal with NGS data, thanks a lot for those > people how contribute to all those nice packages in BioC. I just have some > features request for the GappedAlignments, probably it's already there or > it's not a good practice to do it in certain way, please feel free to let me > know. > > I like features from both scanBam or readBamGappedAlignments, just sometime > I need to write my own script trying to combine information from those two > function and make a "general" granges to work with. So I am wondering if > there is any way to do it in a neat way or is there a plan to implement > similiar features? > > - Including more element meta data with GappedAlignments > - there is "which" in readBamGappedAlignments, can I have some thing > like "param" or "what" to get more info from bam file and associate them > with Gapped reads. > - When doing the coerce from GappedAlignement to GRanges, or call > granges() on GappedAlignments object, it only return the minimal > information, "qwidth", "cigar", "ngap" is not included as > elementMetadata. > - Including more pairing information for pair-end RNA-seq > - So I could know the mated information with certain gapped reads, > either plot it as pair-end read or do some computation on it. > - Setting flags for each entry, so I can filter it out based on the > flags, something like from scanBamFlag? > - grglist to transform the data in different way > > If I can get a general data structure which combine all those information > and or features together, that would be nice, I realize it's hard to > combine all information together and make it flexible at the same time , > e.g. you need to deal with how to binding element meta data for paired > entry, probably showing seq1/seq2 to indicate which sequence it's belongs > too? how to handle multiple hits? > > Right now, I am making my own "giant" GRanges object which including all the > information I want, but that's too specific for my work, that's why I am > wondering if there is any plan to combine those neat features together and > bring a more flexible data structure. > > Thanks! > > Tengfei > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Hi Martin, Thanks a lot for these updates! I will try these new features, they are very helpful for what I am doing now. If I have more specific use cases, I will let you know. Thanks again! Tengfei On Tue, Aug 23, 2011 at 3:47 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > Hi Tengfei -- > > We've acted on some of your suggestions (e.g., incorporating any field in > GappedAlignments, making readBamGappedAlignments accept a ScanBamParam() > when Rsamtools 1.5.53 becomes avaiable), thanks! > > We're really interested in hearing from you and others about specific use > cases for paired-end representations, particularly those operations that are > difficult to do with the current GappedAlignments (e.g., the distribution of > insertion sizes could now be easily extracted as ScanBamParam(what="isize", > flag=scanBamFlag(isProperPair=**TRUE, isPrimaryRead=TRUE))). > > So please forward any specific use cases! > > Martin > > > > On 08/09/2011 11:33 AM, Tengfei Yin wrote: > >> Dear all, >> >> I am using GenomicRanges and Rsamtools a lot for my work, they are >> extremely >> helpful and neat packages to deal with NGS data, thanks a lot for those >> people how contribute to all those nice packages in BioC. I just have some >> features request for the GappedAlignments, probably it's already there or >> it's not a good practice to do it in certain way, please feel free to let >> me >> know. >> >> I like features from both scanBam or readBamGappedAlignments, just >> sometime >> I need to write my own script trying to combine information from those two >> function and make a "general" granges to work with. So I am wondering if >> there is any way to do it in a neat way or is there a plan to implement >> similiar features? >> >> - Including more element meta data with GappedAlignments >> - there is "which" in readBamGappedAlignments, can I have some thing >> like "param" or "what" to get more info from bam file and associate >> them >> with Gapped reads. >> - When doing the coerce from GappedAlignement to GRanges, or call >> granges() on GappedAlignments object, it only return the minimal >> information, "qwidth", "cigar", "ngap" is not included as >> elementMetadata. >> - Including more pairing information for pair-end RNA-seq >> - So I could know the mated information with certain gapped reads, >> either plot it as pair-end read or do some computation on it. >> - Setting flags for each entry, so I can filter it out based on the >> flags, something like from scanBamFlag? >> - grglist to transform the data in different way >> >> If I can get a general data structure which combine all those information >> and or features together, that would be nice, I realize it's hard to >> combine all information together and make it flexible at the same time , >> e.g. you need to deal with how to binding element meta data for paired >> entry, probably showing seq1/seq2 to indicate which sequence it's belongs >> too? how to handle multiple hits? >> >> Right now, I am making my own "giant" GRanges object which including all >> the >> information I want, but that's too specific for my work, that's why I am >> wondering if there is any plan to combine those neat features together >> and >> bring a more flexible data structure. >> >> Thanks! >> >> Tengfei >> >> >> > > -- > Computational Biology > > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]]
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