how to align sequences with extra bases in 5'

Question

[hsu]

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.

Answer 1

[swbarnes2]

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

[hsu]

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

[hsu]

My barcodes are 30bp away from 5'.

[GenoMax]

Are those initial 30 bp important/needed?

[hsu]

No, they are not.

[hsu]

No, they are not.