Question

Sort and convert the SAM files to BAM

0

Entering edit mode

5.7 years ago

amitunited0532 ▴ 40

When I going to convert sam to bam file it's showing error like this.

prashant@prashant-07:~/Desktop/histates$ samtools sort -@ 8 -o SRR087416_chrx.bam SRR087416_chrx.sam 
sort: invalid option -- '@'
open: No such file or directory
[bam_sort_core] fail to open file 8
prashant@prashant-07:~/Desktop/histates$

Thank you

samtools RNA-seq NGS • 1.9k views

ADD COMMENT • link updated 7 months ago by Ram 43k • written 5.7 years ago by amitunited0532 ▴ 40

6

Entering edit mode

Hello amitunited0532,

check your version of samtools with samtools --version The @ option was introduced in version 1.0.

fin swimmer

ADD REPLY • link 5.7 years ago by finswimmer 16k

0

Entering edit mode

Try this

samtools sort myfile.bam -o myfile_sorted.bam

ADD REPLY • link updated 5.7 years ago by finswimmer 16k • written 5.7 years ago by k.kathirvel93 ▴ 300

0

Entering edit mode

when i m giving command it's shows error like this.......

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ADD REPLY • link updated 5.7 years ago by finswimmer 16k • written 5.7 years ago by amitunited0532 ▴ 40

0

Entering edit mode

Have you seen my question? Without knowing the version of samtools it's quite hard to help.

Thanks.

fin swimmer

ADD REPLY • link 5.7 years ago by finswimmer 16k

0

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Samtools version: 0.1.9 (r783)

ADD REPLY • link 5.7 years ago by amitunited0532 ▴ 40

1

Entering edit mode

Hello amitunited0532,

this version is nearly 8 years old. Current version is 1.9. Update is realy necessary. Download and install instructions are here.

fin swimmer

ADD REPLY • link 5.7 years ago by finswimmer 16k

0

Entering edit mode

Thank you for giving your valuable time, I have updated samtools and now it's working properly.

ADD REPLY • link 5.7 years ago by amitunited0532 ▴ 40