Question: Must I sort the .bam or .sam file before do the feature count?
0
gravatar for Xiaokang ZH
3.0 years ago by
Xiaokang ZH40
Xiaokang ZH40 wrote:

I saw some people sort the .bam or .sam file got from alignment, before the next step which is feature count. But what's the point of doing that? To speed up the subsequent process?

rna-seq • 1.9k views
ADD COMMENTlink written 3.0 years ago by Xiaokang ZH40
1
gravatar for genomax
3.0 years ago by
genomax80k
United States
genomax80k wrote:

Not necessary but since one needs sorted files for other things I find it convenient to sort upfront.

Automatically sort paired-end reads. Users can provide either location-sorted or name- sorted bams files to featureCounts. Read sorting is implemented on the fly and it only incurs minimal time cost

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by genomax80k
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