Umi-tools are tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. Currently there are 6 commands.

The extract and whitelist commands are used to prepare a fastq containg UMIs +/- cell barcodes for alignment.

whitelist:
Builds a whitelist of the 'real' cell barcodes
This is useful for droplet-based single cell RNA-Seq where the identity of the true cell barcodes is unknown. Whitelist can then be used to filter with extract (see below)

extract:
Flexible removal of UMI sequences from fastq reads.
UMIs are removed and appended to the read name. Any other barcode, for example a library barcode, is left on the read. Can also filter reads by quality or against a whitelist (see above)
The remaining commands, group, dedup and count/count_tab, are used to identify PCR duplicates using the UMIs and perform different levels of analysis depending on the needs of the user. A number of different UMI deduplication schemes are enabled - The recommended method is directional.

group:
Groups PCR duplicates using the same methods available through `dedup`.
This is useful when you want to manually interrogate the PCR duplicates

dedup:
Groups PCR duplicates and deduplicates reads to yield one read per group
Use this when you want to remove the PCR duplicates prior to any downstream analysis

count:
Groups and deduplicates PCR duplicates and counts the unique molecules per gene
Use this when you want to obtain a matrix with unique molecules per gene. Can also perform per-cell counting for scRNA-Seq.

count_tab:
As per count except input is a flatfile

• https://github.com/CGATOxford/UMI-tools

• Module Name: umitools (see the modules page for more information)
• Example files in /usr/local/apps/umitools/example.fastq.gz

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load umitools
[user@cn3144 ~]$ cp /usr/local/apps/umitools/example.fastq.gz . 
[user@cn3144 ~]$ umi_tools extract --stdin=example.fastq.gz --bc-pattern=NNNNNNNNN --log=processed.log --stdout processed.fastq.gz

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load umitools
umi_tools extract --stdin=example.fastq.gz --bc-pattern=NNNNNNNNN --log=processed.log --stdout processed.fastq.gz

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; umi_tools extract --stdin=example.fastq.gz --bc-pattern=NNNNNNNNN --log=processed.log --stdout processed.fastq.gz
cd dir2; umi_tools extract --stdin=example.fastq.gz --bc-pattern=NNNNNNNNN --log=processed.log --stdout processed.fastq.gz
cd dir3; umi_tools extract --stdin=example.fastq.gz --bc-pattern=NNNNNNNNN --log=processed.log --stdout processed.fastq.gz

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module umitools