how can I get alignment quality from bam index file?

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3.5 years ago

microorganism_001 ▴ 30

Can I get basic statics of a genome alignment with a BAM index file with samtool or any other tool in linux? Is there a need for BAM file mandatory because I did all tasks in the galaxy and it produces huge data.

NGS samtools galaxy • 931 views

ADD COMMENT • link updated 18 months ago by Ram 44k • written 3.5 years ago by microorganism_001 ▴ 30

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I doubt the index contains any of that data.

ADD REPLY • link 3.5 years ago by swbarnes2 14k

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Yes, don't have. Do I need to download the datasets also? I think I have to step into the galaxy. Could you tell me if I want to get the information about alignment which command will helpful in samtool ?

ADD REPLY • link 3.5 years ago by microorganism_001 ▴ 30

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samtools idxstats your.bam. You will need the aligned/sorted BAM file and index that goes with it.

ADD REPLY • link 3.5 years ago by GenoMax 148k

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