the output file of repair

Question

[yueli7]

Hello,

I ran repair which is in Subread package.

The output file is utFiles. What is this file? What is the format of this file?

Thanks!

./repair -i 2-pass_6Aligned.sortedByCoord.out.bam inFormat="BAM" \
        -outFiles 2-pass_6Aligned.sortedByCoord.out.bam.repair, \
        addDummy=TRUE, fullData=TRUE, compress=FALSE,nthreads=8

Finished scanning the input file. Processing unpaired reads.

All finished in 13.41 minutes
Total input reads: 141284712 ; Unpaired reads: 50222

[GenoMax]

You did not need to run repair as was discussed in the last thread you started: program repair in featureCounts

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Answer 1

[h.mon]

If you are going to ignore advice, please at least read the documentation:

-o <string> Name of output file. The output file is in BAM format.

[yueli7]

Thank you for your response!

In my command, the outputFiles should be 2-pass_6Aligned.sortedByCoord.out.bam.repair.

But right now the name is utFiles, and I can not to open it in any way. It is gzip file and 35.2G.

Thank you!

[Ram]

That's because -outFiles was read by the program as -o utFiles. Treat it as you would any output from the tool, the filename/extension never truly makes a difference to the operating system. The output of repair is a BAM file, from the manual.

Also, it's a little weird to ask h.mon further questions after ignoring his previous advice. At least give him a reason why you discarded his advice.