Question: Sorting bam file in mac OS
1
gravatar for Za
3 months ago by
Za50
Za50 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 3 months ago by igor6.5k • written 3 months ago by Za50
3
gravatar for genomax
3 months ago by
genomax54k
United States
genomax54k wrote:

Do

samtools sort  -o SRR1593424_sorted SRR1593424.bam
ADD COMMENTlink written 3 months ago by genomax54k
3
gravatar for igor
3 months ago by
igor6.5k
United States
igor6.5k 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 3 months ago • written 3 months ago by igor6.5k
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