program repair in featureCounts

Question

[yueli7]

Hello,

I try to use featureCounts to summarize the human pair-end read.

The manual of Subread said "We also provide an utility program repair to allow users to pair up the reads before feeding them to featureCounts".

Where is the program "repair"?

Thanks in advance!

[h.mon]

How did you map your reads? Most likely you don't need to repair the bam file.

How did you install Subread? The repair program is under $SUBREAD_FOLDER/bin/utilities/.

[yueli7]

Thanks!

I ran STAR to map my reads.

The output files are: 2-pass_Aligned.out.bam, 2-pass_Aligned.sortedByCoord.out.bam, 2-pass_Aligned.toTranscriptome.out.bam.

I just want to double check: I will use 2-pass_Aligned.sotredByCoord.out.bam to do the following work, it that correct?

Thanks!

Answer 1

[h.mon]

Indeed, you don't need to repair your reads, and yes, use the "2-pass_Aligned.sotredByCoord.out.bam" with featureCounts. By the way, you could have used STAR --quantMode GeneCounts to get a table of counts similar to that of featureCounts.

[yueli7]

Thanks for your great help!

[WouterDeCoster]

The reaction from h.mon got moved to an answer, so can you accept it if it solves your question?