Hi Wei, I have one more question. (I hope its just one more). Is there a way to have subread use a qual file in addtion to a csfasta file, or would I need to convert to some kind of csfastq? Simon On Mon, Jul 29, 2013 at 8:44 PM, Wei Shi <shi@wehi.edu.au> wrote: > Hi Simon, > > I have just added 'color2base' option to the align function in Rsubread to > let it access the color base conversion facility in Subread (-b option). I > have committed it to the devel branch of Rsubread (v1.11.9) and it should > be available to you in a couple of days. > > Thanks, > Wei > > > On Jul 30, 2013, at 6:11 AM, Simon Coetzee wrote: > > Thanks for the help, everything is running smoothly now. > Only one more question, is there an option in Rsubread equivalent to "-b" > in Subread (to output the sam file in basespace format, when starting from > colorspace fasta)? > > Thanks again, > > Simon Coetzee > > Centro Regional de Hemoterapia > Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto > Universidade de São Paulo > > > > On Fri, Jul 26, 2013 at 11:20 PM, Wei Shi <shi@wehi.edu.au> wrote: > >> Dear Simon, >> >> Yes, the F3/F5 protocol is supported by Subread. You will need to set >> PE_orientation="ff" when you run align or subjunc functions. This will tell >> the alignment programs that the two reads from the same pair are on the >> same strand and they can then be handled properly. >> >> Sorry the documentation did not provide enough details about how to map >> such reads. I have just added more descriptions to this to the help pages >> and user guide to make them more clearer. >> >> Best wishes, >> >> Wei >> >> On Jul 27, 2013, at 6:31 AM, Simon Coetzee wrote: >> >> > I have some paired end SOLID sequencing data, the protocol using F3/F5 >> > fragments (not the simpler F3/R3). Both fragments come from the same >> > strand. Some of the nuances are explained here: >> > http://www.biostars.org/p/48597/ >> > >> > Having read the manual for Rsubread, its clear that it can handle SOLID >> > sequencing, colorspace reads, and paired end sequencing. However, is >> the >> > F3/F5 protocol directly supported, or will there have to be >> preprocessing >> > of the F5 fragments? >> > >> > Simon Coetzee >> > -- >> > Centro Regional de Hemoterapia >> > Hospital das Clínicas da Faculdade de Medicina de *Ribeirão Preto >> > *Universidade de São Paulo >> > >> > -- >> > >> > No trees were killed to send this message, but a large number of >> electrons >> > were terribly inconvenienced. >> > >> > [[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 >> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the >> addressee. >> You must not disclose, forward, print or use it without the permission of >> the sender. >> ______________________________________________________________________ >> > > > > -- > > No trees were killed to send this message, but a large number of electrons > were terribly inconvenienced. > > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:17}}

Hi Simon, Yes, if you convert your data to csfastq format Subread will be able to use the quality score info for the alignment. Cheers, Wei On Sep 3, 2013, at 2:30 AM, Simon Coetzee wrote: > Hi Wei, > > I have one more question. (I hope its just one more). Is there a way to have subread use a qual file in addtion to a csfasta file, or would I need to convert to some kind of csfastq? > > Simon > > > On Mon, Jul 29, 2013 at 8:44 PM, Wei Shi <shi@wehi.edu.au> wrote: > Hi Simon, > > I have just added 'color2base' option to the align function in Rsubread to let it access the color base conversion facility in Subread (-b option). I have committed it to the devel branch of Rsubread (v1.11.9) and it should be available to you in a couple of days. > > Thanks, > Wei > > > On Jul 30, 2013, at 6:11 AM, Simon Coetzee wrote: > >> Thanks for the help, everything is running smoothly now. >> Only one more question, is there an option in Rsubread equivalent to "-b" in Subread (to output the sam file in basespace format, when starting from colorspace fasta)? >> >> Thanks again, >> >> Simon Coetzee >> >> Centro Regional de Hemoterapia >> Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto >> Universidade de São Paulo >> >> >> >> On Fri, Jul 26, 2013 at 11:20 PM, Wei Shi <shi@wehi.edu.au> wrote: >> Dear Simon, >> >> Yes, the F3/F5 protocol is supported by Subread. You will need to set PE_orientation="ff" when you run align or subjunc functions. This will tell the alignment programs that the two reads from the same pair are on the same strand and they can then be handled properly. >> >> Sorry the documentation did not provide enough details about how to map such reads. I have just added more descriptions to this to the help pages and user guide to make them more clearer. >> >> Best wishes, >> >> Wei >> >> On Jul 27, 2013, at 6:31 AM, Simon Coetzee wrote: >> >> > I have some paired end SOLID sequencing data, the protocol using F3/F5 >> > fragments (not the simpler F3/R3). Both fragments come from the same >> > strand. Some of the nuances are explained here: >> > http://www.biostars.org/p/48597/ >> > >> > Having read the manual for Rsubread, its clear that it can handle SOLID >> > sequencing, colorspace reads, and paired end sequencing. However, is the >> > F3/F5 protocol directly supported, or will there have to be preprocessing >> > of the F5 fragments? >> > >> > Simon Coetzee >> > -- >> > Centro Regional de Hemoterapia >> > Hospital das Clínicas da Faculdade de Medicina de *Ribeirão Preto >> > *Universidade de São Paulo >> > >> > -- >> > >> > No trees were killed to send this message, but a large number of electrons >> > were terribly inconvenienced. >> > >> > [[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 >> >> ______________________________________________________________________ >> The information in this email is confidential and intended solely for the addressee. >> You must not disclose, forward, print or use it without the permission of the sender. >> ______________________________________________________________________ >> >> >> >> -- >> No trees were killed to send this message, but a large number of electrons were terribly inconvenienced. > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:22}}