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how to align sequences with extra bases in 5'

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
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written by hsu • hsu

1 answer

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

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written by swbarnes2 swbarnes2

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

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written by hsu • hsu

My barcodes are 30bp away from 5'.

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written by hsu • hsu

Are those initial 30 bp important/needed?

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written by GenoMax GenoMax

No, they are not.

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written by hsu • hsu

No, they are not.

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written by hsu • hsu

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