Why are my bed graphs and HTseq-count files not agreeing?
1
1
Entering edit mode
5.3 years ago
shanasabri ▴ 40

When I load my bed graphs into IGV I see that 40/96 cells have signal on Xist. However when I look at my counts output from HTseq-counts for the same data I only see about 20 cells with Xist signal. Any ideas why this is? 

My HTseq-count command: 

    ~/bin/htseq-count \
            --format=bam \
            --order=name \
            --stranded=no \
            --minaqual=0 \
            --type=exon \
            --mode=union \
            --idattr=gene_id \
            {outdir}/{s}_aligned_sortedByName.bam \
            {GTF} \
        > {outdir}/{s}.counts
    

My Bedtools command: 

    ~/bin/bedtools \
            genomecov \
            -split \
            -bg \
            -ibam {outdir}/{s}_aligned_sortedByCoord.bam \
            -g {CHROMINFO} \
        > {outdir}/{s}.bedgraph


I should mention that when I load the bed graphs into IGV I auto scale all tracks. 

htseq bedgraphs • 1.4k views
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1
Entering edit mode
5.3 years ago

Most likely the difference is due to htseq-count excluding multimappers and secondary alignments, which will occur regardless of what the minimum MAPQ is set to.

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