Get length of the alignment from bam file
1
0
Entering edit mode
6.0 years ago
David ▴ 230

Hi, I would like to know if it is it possible to get the read length of the higher alignment in a bam file having more than 85% identity.

For example an output with this fields:

  • Read_length
  • Alignment_length
  • Percent_identity

thanks

bam • 4.0k views
ADD COMMENT
0
Entering edit mode

You can do this with pysam. Do you have any (Python) coding experience?

ADD REPLY
0
Entering edit mode

I´m more of a perl guy but can give it a try

ADD REPLY
3
Entering edit mode
6.0 years ago

using bioalcidaejdk : http://lindenb.github.io/jvarkit/BioAlcidaeJdk.html

ADD COMMENT
0
Entering edit mode

Hi, Does bioaclidaejdk get the output of those three column in same order as present in sam file. So can i apped read id information row by row to the output.?

ADD REPLY

Login before adding your answer.

Traffic: 2633 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