Dear sequencing experts,
I recently run into a problem when I use samtools to sort RNA sequencing BAM files by name. I had totally 260 bam files to run, 15 of them complained "bgzfcheckEOF: Invalid argument". For each of these 15, it generates several files XXXXXXX.0001.bam, XXXXXXX.0002.bam, XXXXXXX.0003.bam etc files but refused to merge them together as they other 250 did.
The wired thing is that I checked my header and they look OK. Further more, I reran these 15 samples and they magically worked!! Then I got confused. What might be the problem? Does anybody have any idea why this might happen? I began to worry whether I should rerun all other 250 samples to make sure they didn't make any mistake.
The code I used are simily: samtools sort -n XXXXXX.bam XXXXXX.sorted.bam
Any suggestion is well appreciated!
hi, Kronenberg! If I want to check my sam/bam file's integrity, what command should I use? What does "Check the hex signatures on the end of the bam" mean? Thanks.