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the output file of repair

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
rna-seq
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updated by Ram Ram • written by yueli7 yueli7

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

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written by Ram Ram

1 answer

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.

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written by h.mon h.mon

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!

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written by yueli7 yueli7

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.

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written by Ram Ram

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