how can I get alignment quality from bam index file?
0
0
Entering edit mode
3 months ago
abhisek061 ▴ 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.

galaxy NGS samtool • 290 views
ADD COMMENT
0
Entering edit mode

I doubt the index contains any of that data.

ADD REPLY
0
Entering edit mode

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
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1999 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6