How to move UMI tags to the header

Question

[newbinf]

I have complete sequences from 10x Chromium that look like the following:

|----my 16 bp cell barcode----|---8bp 10x UMI---|--SO--|-------------------cDNA (100 bp)----------------------| SO = switch oligo

The reads are demultiplexed and don't have the Illumina barcodes in the sequence. I want to map the cDNA (sequence of interest), however I want to preserve the data provided by my barcode, 10x UMI, and switch oligo (about 40 bp). This is so I can identify duplicates and which cell each read originated from.

I can found trimming softwares (cutadapt and trimmomatic) that can delete the the 40bp. However, because I want to retain this information, I do not want to simply trim the sequences. On the other hand, keeping the sequences have lead to 70-90% not mapping because of the 40bp of non-genetic information.

I have thought about 'cutting and pasting' the information into the header, but am not aware of a program that already does this.

How to I align these reads while preserving the data provided by the 40bp barcodes?

Answer 1

[GenoMax]

Have you looked at umitools (https://github.com/CGATOxford/UMI-tools )?

[newbinf]

After skimming through the documentation, this looks like what I need. Thank you!