User: rodri

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rodri10
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Posts by rodri

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Comment: C: Different coverage on RNA-Seq strands
... Unfortunately that is not the problem: $ bamCoverage --version bamCoverage 2.5.3 I've tried with another S pombe RNA-seq dataset from our lab and it also makes this assymmetry in coverage. I'm trying now with another pombe experiment (GSE97747), where the authors tell they do the cover ...
written 13 months ago by rodri10
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Comment: C: Different coverage on RNA-Seq strands
... You mean bamCoverage? The read pairs seem ok, more or less the same number of forward and reverse reads: $ samtools view -c -F 16 -@ max SRR2833398.bam 3853154 $ samtools view -c -f 16 -@ max SRR2833398.bam 3561999 Which make good pairs if i represent them all on SRR2833398.bam on ...
written 13 months ago by rodri10
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Comment: C: Different coverage on RNA-Seq strands
... Yes, we checked in IGV and it just confirms the output of bamCoverage, >10x scale in forward respect to reverse strand ...
written 13 months ago by rodri10
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Different coverage on RNA-Seq strands
... Hi, We have tried several samples from an experiment in GEO ([Series GSE74411][1]), especifically SRA accessions SRR2833398, SRR2833399 and SRR2833400; and in all of them we have a larger number of reads alignments to forward (>90%) than to reverse (<10%) strands. The experiment says it uses a ...
paired-end rna-seq stranded written 13 months ago by rodri10 • updated 9 months ago by Mike30

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