Question: many read aligned to the same position but with different variants
0
gravatar for yliueagle
5 weeks ago by
yliueagle220
France
yliueagle220 wrote:

(Please open this link if image not displayed: https://ibb.co/mHYH8NC

I have two questions related to the following alignment from a single sequencing sample of a cell line:

(1) are the reads in the bottom represent PCR duplicates, as they are aligned exactly to the same position (2) if they are duplicates, why there are so many different variants among them? (e.g,. at the position near 60795540

Thanks for your answer!

enter image description here

alignment duplicates reads • 133 views
ADD COMMENTlink modified 5 weeks ago by genomax92k • written 5 weeks ago by yliueagle220

are the reads in the bottom represent PCR duplicates, as they are aligned exactly to the same position

We don't see the full reads but there are too many differences in them just in this region to be PCR duplicates. You would normally have the same start/end with a defined number (small) of differences in them.

Run a tool like clumpify.sh if you really want to identify duplicates: A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files

ADD REPLYlink written 5 weeks ago by genomax92k

Thanks for your answer. Here I updated the figure. These reads mapped exactly to the same region except that they have different variants, especially at the position near 60795540

ADD REPLYlink written 5 weeks ago by yliueagle220

These reads mapped exactly to the same region except that they have different variants

Then they don't quite fit the definition of PCR duplicates. Perhaps you are allowing too many errors when reads are originally aligned, which allows these reads to map here (even if they are not from this region). Is there any soft-clipping happening that we can't see in that image? If you want to identify PCR duplicates then use the clumpify method.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax92k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1180 users visited in the last hour