Hi Everyone,
I want to use bwa mem to align my fastq files to the ref genome.
My fastq files are .bz2 compressed. Something like this a_1.fastq.bz2, a_2.fastq.bz2
Is there a way bwa mem can take compressed fastq files as input or on the fly on command line???
I am using this command
This gives me an error but when I de compress it , the above command runs fine.
I have a lot of .fastq.bz2 files and would want to wrap them into a script for alignment. Is there a way I don't have to de compress the .bz2 files and still can run bwa.
Hope to hear from you soon
Regards
Varun
I want to use bwa mem to align my fastq files to the ref genome.
My fastq files are .bz2 compressed. Something like this a_1.fastq.bz2, a_2.fastq.bz2
Is there a way bwa mem can take compressed fastq files as input or on the fly on command line???
I am using this command
Code:
/apps/bwa mem -t 12 -v 1 -a -M /indexes/bwa/ref.fa a_1.fastq.bz2 a_2.fastq.bz2 > aln_pe.sam
I have a lot of .fastq.bz2 files and would want to wrap them into a script for alignment. Is there a way I don't have to de compress the .bz2 files and still can run bwa.
Hope to hear from you soon
Regards
Varun
Comment