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I was looking how to take readcount from ATAC seq data , this post which suggested to use bedtools and featurecounts to take out readcounts .But multiBamSummary seems to be pretty straight forward. Now I have my count file but only issue is there are no gene names. So now is it possible to annotate these chromosome regions? if so how ?

Any suggestion or help would be highly appreciated

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Assuming you used a BED file as input then the output is in the same order, so just merge the two files together.

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  • $\begingroup$ i used bam files in case of bed files but yes the orders are same .But would that help me in annotating the region ? $\endgroup$
    – kcm
    Nov 25 '19 at 8:37
  • $\begingroup$ I assume you used multiBamSummary BED-file, did you use multiBamSummary bins instead? $\endgroup$
    – Devon Ryan
    Nov 25 '19 at 8:45
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    $\begingroup$ They're bins of the size you specified that tile the genome then. $\endgroup$
    – Devon Ryan
    Nov 25 '19 at 8:55
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    $\begingroup$ Overlap/intersect them with a GTF file. $\endgroup$
    – Devon Ryan
    Nov 25 '19 at 8:58
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    $\begingroup$ "Conceptual question" (a doubt is generally not something one "has" in English). I'd just simply map things to the GTF file. $\endgroup$
    – Devon Ryan
    Nov 25 '19 at 10:20

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