How to call snps on sequencing data that contains UMIs
0
0
Entering edit mode
5 months ago

Hello,

I asked the question on the help forum on Galaxy, but got no answer, so I'm trying my luck here.

I would like to analyze fastQ files from MiSeq Illumina. For this I want to do a DNA alignment on a reference genome (hg38) and then a polymorphism detection at known positions (I have a bed file with all the positions) and get a VCF file.

I don't know which tools to use on the web plateform of Galaxy. One of the problem is that the sequencing was done with UMIs, for low-intensity polymorphism detection (less PCR and sequencing errors). I don’t know what tools to use to do the alignment taking into account the UMIs. So I have 4 fastQ files : R1 and R2 because it's a double end sequencing, and if necessary, I1 and I2 which contain the indexs and UMIs sequences (I1 = index I7 + UMI and I2 = index I5).

Thank you

Galaxy UMI DNA-seq • 220 views
ADD COMMENT
0
Entering edit mode

I have changed the title of the post to better reflect the question. Galaxy is not all that relevant, as that is not a tool but a platform, one still need to know what tools to use

ADD REPLY

Login before adding your answer.

Traffic: 1826 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