Question

How createSet from reduced "paire-ed" sequencing on MeDIPS?

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pertille • 0

@pertille-9104

Last seen 5.8 years ago

Sweden

I'm trying to create a set with my .BAM file that was generated from reduced "paired end" sequencing (using restriction enzyme), I can easily run it as "single end", but when I add "paired = T" in the command, this message appears:

> MeDIP_RJF_AV163=MEDIPS.createSet(file=RJF_AV163, BSgenome=genome, extend=extend, shift=shift, uniq=uniq, window_size=ws, chr.select=chr_all, paired=T)
Reading bam alignment RJF_AV163_cleaned_sorted.bam
considering  chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chr23 chr24 chr25 chr26 chr27 chr28 chr32 chrW chrZ  using bam index
Total number of imported first mate reads in properly mapped pairs: 3855090
scanBamFlag: isPaired = T, isProperPair=TRUE , hasUnmappedMate=FALSE, isUnmappedQuery = F, isFirstMateRead = T, isSecondMateRead = F
Mean insertion size: 148.6603 nt
SD of the insertion size: 71.82463 nt
Max insertion size: 582 nt
Min insertion size: 21 nt
Creating GRange Object...
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
  solving row 2010: negative widths are not allowed

Some one knows how to figure out this problem?

medips R input files • 1.3k views

ADD COMMENT • link updated 8.8 years ago by Lukas Chavez ▴ 570 • written 8.8 years ago by pertille • 0

score 2 · Accepted Answer · 2016-02-09

Dear Pertille, in bam files generated by bwa, the first mate of a pair can be the 'left' or the 'right’ mate. This can result in negative widths calculated within MEDIPS. To overcome this issue, we have added the parameter bwa to the MEDIPS.createSet() and MEDIPS.createROIset() functions. Therefore, please set bwa=TRUE when processing paired end data (paired=T) mapped by bwa (or by other aligners which handle left and right mates the same way). All the best, Lukas On 09 Feb 2016, at 12:18, pertille [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User pertille<https: support.bioconductor.org="" u="" 9104=""/> wrote Question: How createSet from reduced "paire-ed" sequencing on MeDIPS?<https: support.bioconductor.org="" p="" 78053=""/>: I'm trying to create a set with my .BAM file that was generated from reduced "paired end" sequencing (using restriction enzyme), I can easily run it as "single end", but when I add "paired = T" in the command, this message appears: > MeDIP_RJF_AV163=MEDIPS.createSet(file=RJF_AV163, BSgenome=genome, extend=extend, shift=shift, uniq=uniq, window_size=ws, chr.select=chr_all, paired=T) Reading bam alignment RJF_AV163_cleaned_sorted.bam considering chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chr23 chr24 chr25 chr26 chr27 chr28 chr32 chrW chrZ using bam index Total number of imported first mate reads in properly mapped pairs: 3855090 scanBamFlag: isPaired = T, isProperPair=TRUE , hasUnmappedMate=FALSE, isUnmappedQuery = F, isFirstMateRead = T, isSecondMateRead = F Mean insertion size: 148.6603 nt SD of the insertion size: 71.82463 nt Max insertion size: 582 nt Min insertion size: 21 nt Creating GRange Object... Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 2010: negative widths are not allowed Some one knows how to figure it out this problem? ________________________________ Post tags: medips, R, input files You may reply via email or visit How createSet from reduced "paire-ed" sequencing on MeDIPS?