samtools sort error
Hello everyone, I am getting an error by sorting sam file to bam files, please attached is the screenshot
this is the code I use
samtools sort pf382wt-bcat.sam > pf382wt-bcat.bam
Failed to open file pf382wt-bcat.sam samtools view: failed to open "pf382wt-bcat.sam" for reading: Exec format error
the ligament was performed with bowtie
Do you guys have any suggestion? thank you
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Morris_Chair
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are you sure ? the error message specify it was about
samtools view.about the error Exec format error. How did you get the samtools executable ? aren't you mixing a program compiled for 32 bits on a 64 bits computer ? (or the other way around...)
Hi Pierre, It doesn't like anything I do with samtools on this files, I don't work on my own computer but I use the workstation of the research institute. All tools are already installed there. To get the executable for samtools, I used bwa with this cmd line
thanks for help
The usage of
bwa memandbowtie2are different, you'd better refer to the manual ofbwaorbowtie2at first.Oh I didn't know that the usage was different, I used bwa because I read that is better for alignment of ChIP-seq experiment compared to bowtie2
but then how can I convert this sam file to bam from bwa?
thank you
ok probably I solved, I m doing again the alignment by using this code to get directly the bam file
finger crossed.. and thank you :)