Hi-C Pro
1
0
Entering edit mode
8 weeks ago
SEJAL • 0

I used Hi-C pro to align the hic raw reads and got very less alignment percentage, i.e. around 40-50%, what could be the possible reasons?

I used the bowtie2 indexed GRCh38 genome; downloaded from here (https://benlangmead.github.io/aws-indexes/bowtie)

hicpro alignment hic • 398 views
ADD COMMENT
2
Entering edit mode
12 days ago
kalavattam ▴ 310

An alignment percentage of 40–50% is fairly typical for Hi-C data. Several factors contribute to this, including the fact that Hi-C libraries contain a sizable fraction of chimeric reads resulting from ligation events between distant genomic regions. Also, random ligation artifacts (e.g., misligated fragments) can reduce the number of valid alignments. For more details, you can see this (now classic) review: Lajoie, Dekker, and Kaplan, The Hitchhiker's guide to Hi-C analysis: practical guidelines, Methods 2015 (PMID: 25448293).

ADD COMMENT

Login before adding your answer.

Traffic: 2509 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