Question: Sorting bam file in mac OS
1
gravatar for Za
6 days ago by
Za10
Za10 wrote:

Hi,

I don't know why I can't sort my bam files

dhcp179185:unknown$ samtools sort SRR1593424.bam SRR1593424_sorted
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)
  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]
  -n         Sort by read name
  -t TAG     Sort by value of TAG. Uses position as secondary index (or read name if -n is set)
ADD COMMENTlink modified 6 days ago by igor6.0k • written 6 days ago by Za10
3
gravatar for genomax
6 days ago by
genomax47k
United States
genomax47k wrote:

Do

samtools sort  -o SRR1593424_sorted SRR1593424.bam
ADD COMMENTlink written 6 days ago by genomax47k
3
gravatar for igor
6 days ago by
igor6.0k
United States
igor6.0k wrote:

Did you read the error message?

Use -T PREFIX / -o FILE to specify temporary and final output files

You did not specify either.

I think you are copying the command written for a specific version of samtools, but the version you have is different and requires slightly different parameters.

ADD COMMENTlink modified 6 days ago • written 6 days ago by igor6.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1041 users visited in the last hour