Hi all,
I am working on TCGA WGS.. and the files are huge..
Is there a way to copy all the reads directly from the bam file without using samtools and bam2fastx (from tophat)?
Right now i am using:
samtools sort -n *.bam *.bam.sorted
bam2fastx -q -Q -A -P -o out.fq *.bam.sorted.bam
and it is very slow..
i dont mind to stay in binary mode, and i am not using the quality + the order isnt relevant..
Or,
to spped up what i am doing now..
Thanks!
I am working on TCGA WGS.. and the files are huge..
Is there a way to copy all the reads directly from the bam file without using samtools and bam2fastx (from tophat)?
Right now i am using:
samtools sort -n *.bam *.bam.sorted
bam2fastx -q -Q -A -P -o out.fq *.bam.sorted.bam
and it is very slow..
i dont mind to stay in binary mode, and i am not using the quality + the order isnt relevant..
Or,
to spped up what i am doing now..
Thanks!
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