HI optional field in paired-end reads
0
0
Entering edit mode
13 months ago
roccostorace ▴ 30

Hi all,

I'm working on RNA-seq on BAM file (single read) containing as optional fields the NH and HI tags, used to make featureCounts analisys. For example i have NH:i:6 and 1<=HI<=6.

From https://samtools.github.io/hts-specs/SAMtags.pdf the tag definitions are:

NH:i:count Number of reported alignments that contain the query in the current record. HI:i:i Query hit index, indicating the alignment record is the i-th one stored in SAM.

In case of paired-end reads with multiple alignments, I have a doubt on how these tags work?

Example:

read1 has 4 alignments read2 has 7 alignments

So i I'll see NH:i:4 for read1 and NH:i:7 for read2, or one NH:i:11 (7+4). The same with HI, i'll see 1<=HI<=4 for read1 and 1<=HI<=7 for read2, or one 1<=HI<=11 (7+4)?

HI tag optional field NH • 261 views
ADD COMMENT

Login before adding your answer.

Traffic: 2149 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