Please disregard my previous message. It finally dawned on me that the
additional file was not output from samtools, but from an unrelated
analysis pipeline being run on the data. I hadn't realized the other
pipeline had been started yet, so its output existing caught me by
surprise. I apologize for the confusion.
Sincerely,
Jason Kost
On Tue, Aug 28, 2018 at 12:32 PM, Kost, Jason <jk...@worcester.edu> wrote:
> Currently trying to convert some BAM files back to FASTQ to perform
> alignment with known parameters. Everything seems to be working, but there
> is a file being generated by samtools which I can find no documentation or
> explanation of. Running the following command:
>
> samtools fastq -0 ${fname}_other.fq.gz -1 ${fname}_1.fq.gz -2
> ${fname}_2.fq.gz -@ 10 ${i} --reference ../../reference/hg19/GRCh38.
> p12.fna.gz
>
> For output files I'm getting:
>
> fname_1.fq.gz
> fname_2.fq.gz
> fname_other.fq.gz
>
> Which is what I expect. However, I am also getting
>
> fname_soft.fastq.gz
>
> Any ideas what this fourth file contains and/or why it's being generated?
> From the name, my first guess would be that it contains the soft-clipped
> reads from the BAM file. If so, are the non-clipped reads also being placed
> in the _1 and _2 files? As far as I can find, there is no mention of the
> _soft file anywhere in the documentation (either for the fastq command or
> any other command). Any insight would be greatly appreciated.
>
> Sincerely,
> Jason Kost
>
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