Sort and convert the SAM files to BAM
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6.3 years ago

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 • 2.1k views
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6
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Hello amitunited0532,

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

fin swimmer

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Try this

samtools sort myfile.bam -o myfile_sorted.bam
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when i m giving command it's shows error like this.......

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

Thanks.

fin swimmer

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Samtools version: 0.1.9 (r783)

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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

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

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