I see. Thank you.
No. I didn't receive any error messages.
• 0 views
•
link
written
by
Bioinf_Questions •
Splitted sorted BAM files with samtools
Hello. I'm trying to use the command "sort" of samtools (ex: samtools sort alignment.bam -o alignment.sorted.bam), but for some reason, instead of generating one single sorted file (ex: alignment.sorted.bam) it generates many files (ex: alignment.sorted.bam.0000.bam, alignment.sorted.bam.0001.bam, alignment.sorted.bam.0002.bam, ..., alignment.sorted.bam.0020.bam). The odd thing is that I had used the exact same command before for a few data of the same batch and it generated a single file. Does anyone have any idea what could be happening and how do I solve this? I'm also thinking of merging the files, if I can't solve it. How do I find out the correct order to merge? Thanks in advance.
• 1,303 views
•
link
written
by
Bioinf_Questions •
1 answer
These are intermediate/temporary files that are created once the chunk of sorted reads exceeds the allocated (-m) memory taht is used to store them in RAM. They should be automatically merged into a single file and then cleaned up unless your job got killed for any reason. Any error messages?
Log in to answer this question.
More posts like this
-
DESeq2 input file
written by Bioinf_Questions •
-
Plotting .tab/.bam file
written by zack.henning •
-
bowtie2 piped to samtools created many samtools.tmp.bam files, how to get the single .bam file?
written by dongchenchen •
-
how to use samtools sort correctly?
written by mlemusfuentes •
-
Samtools sort memory issues
written by bioinfo •
-
samtools merge warning
written by lshepard
-
Why Bam File Been Seperated By Samtools
written by Chen Sun
-
Problem With Sorting Bam File: Samtools
written by lyfsa •
-
Samtools Sort Eof Error
written by zhaoni153 •
-
Samtools: "Too Many Open Files"
written by Zhshqzyc •
