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how to determine strand from tophat output for paired-end RNA-seq data jay2008 Bioinformatics 1 05-30-2012 04:46 AM
strand specific wig files frymor Bioinformatics 0 07-27-2011 10:47 PM
What is this strand specific pair-end RNA-seq data? xhuister Bioinformatics 2 09-14-2010 06:34 AM

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Old 06-03-2012, 11:00 AM   #1
ulitskyi
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Default .wig files for strand-specific paired-end RNA-Seq

Hi,

Is there a simple way to make strand-specific .wig file (i.e., a separate track for + and - strand) from paired-end data (where the second read maps to the other strand)? genomeCoverageBed doesn't seem to handle this well. Any alternatives?

Igor.
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Old 06-03-2012, 06:00 PM   #2
Dario1984
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It's quick using R with the packages Rsamtools, GenomicRanges, and rtracklayer.

Code:
library(Rsamtools)
library(rtracklayer)
myReads <- readGappedAlignments("RNAseqMapping.bam")
coveragePlus <- coverage(myReads[strand(myReads) ==  '+'])
export(coveragePlus, "RNAplus.wig")
coverageMinus <- coverage(myReads[strand(myReads) ==  '-'])
export(coverageMinus, "RNAminus.wig")
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Old 06-07-2012, 12:47 PM   #3
ulitskyi
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Thanks! But this appears to suffer from the same problem as genomeCoverageBed - I get similar coverage on both strands, because if the transcript is on the + strand, read #2 maps to the - strand, and contributes to the coverage on the - strand... Is there any way around this?
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Old 06-07-2012, 11:01 PM   #4
Dario1984
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Good point. You should ask about it on the Bioconductor mailing list. They implement feature requests quickly.
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Old 06-12-2012, 11:27 PM   #5
frozenlyse
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Just flip the strand of the #2 reads
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