Question: how to align sequences with extra bases in 5'
0
gravatar for hsu
9 months ago by
hsu10
hsu10 wrote:

Hi, my sequecing data contains 30 extra base pairs in the 5' which also contain UMI information. First, I want to map these reads to a reference genome and then I want to stastics the UMI information. How should I set mapping defaults? Does 30 extra bps interfere the mapping process?

My UMI information is not in the start point of a reads. They are 30bp away from 5'.

Thanks for your answers.

alignment umi • 210 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by hsu10
0
gravatar for swbarnes2
9 months ago by
swbarnes27.5k
United States
swbarnes27.5k wrote:

The simplest thing to do is use umi-tools to pull the umi off of the read, and put it in the read name. Then align as usual, and then run mi-tools to go through the bam and remove excess reads based on map position and umi sequence

ADD COMMENTlink written 9 months ago by swbarnes27.5k

My library is single-fragment size, 310bp. Does this situation be suitble to the methods you mentioned?

ADD REPLYlink written 9 months ago by hsu10

My barcodes are 30bp away from 5'.

ADD REPLYlink written 9 months ago by hsu10

Are those initial 30 bp important/needed?

ADD REPLYlink written 9 months ago by genomax78k

No, they are not.

ADD REPLYlink written 9 months ago by hsu10

No, they are not.

ADD REPLYlink written 9 months ago by hsu10
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