Umi_tools regex blank output

Question

[amyruthvandiver]

Hello,

I am looking for assistance using regex for umi extraction with umi tools.

My reads contain a 23 bp universal sequence followed by a 12 bp umi.

I know these are at the 5' end of my read, because when I extract the first 35 bp with umi_tools to visually inspect, the sequences are exactly as expected.

However, when I attempt to use regex to pull out the umi (which I would prefer to do for multiple reasons), no matches are found.

The code I am using:

umi_tools extract --stdin=test.filt.fastq \
--extract-method=regex\
--bc-pattern='(?P<discard_1>TCTTACGATTACGCCAACCACTG{e<=2})(?P<umi_1>.{12})'--stdout test.processed.fastq

Any guidance is greatly appreciated!

Thank you

Answer 1

[Matthias Zepper]

I think, you may be missing the part of the regex that does match the remainder of the reads (e.g. .* or .{1,120} ): --bc-pattern='(?P<discard_1>TCTTACGATTACGCCAACCACTG{e<=2})(?P<umi_1>.{12}).*'

Answer 2

[i.sudbery]

You need a space between (?P<discard_1>TCTTACGATTACGCCAACCACTG{e<=2})(?P<umi_1>.{12}) and --stdout currently the pattern is being parsed as including the --stdout, and since none of your reads include --stdout they are being rejected. A .* isn't needed, but wouldn't hurt.

[amyruthvandiver]

Thank you SO much! I apologize for not catching that error.