I am trying to extract UMIs using the regex method. The first 10 bases of the read are the UMI.
I am using the following command (according to the UMI-tools docs):
umi_tools extract --extract-method=regex --stdin=trimmed_output_SRR12925922.fastq.gz --bc-pattern='^(?P.{10})' --log=trimmed_output_SRR12925922_processed.log --stdout=processed_trimmed_output_SRR12925922.fastq.gz
I get the following results for a given read:
@SRR12925922.1_ACAACNAGAC 1/1
TCGGAAGAGCACACGTCTGAACTCCAGTCACATTCAGAAATCTCGTATGCCGTCTTCTGCTTT
+
EEAEEEEEAEEEAEEAE//AEE/AE/E/AAEE6AEEAEE6/6/A/EEE//E/EE/E//E<AE/
The UMI sequence extracted by umi_tools doesn't seem to match the first 10 bases of the read.
Does someone have a suggestion what might be wrong?
Hi everyone,
I am trying to extract UMIs using the regex method. The first 10 bases of the read are the UMI.
I am using the following command (according to the UMI-tools docs): umi_tools extract --extract-method=regex --stdin=trimmed_output_SRR12925922.fastq.gz --bc-pattern='^(?P.{10})' --log=trimmed_output_SRR12925922_processed.log --stdout=processed_trimmed_output_SRR12925922.fastq.gz
I get the following results for a given read: @SRR12925922.1_ACAACNAGAC 1/1 TCGGAAGAGCACACGTCTGAACTCCAGTCACATTCAGAAATCTCGTATGCCGTCTTCTGCTTT + EEAEEEEEAEEEAEEAE//AEE/AE/E/AAEE6AEEAEE6/6/A/EEE//E/EE/E//E<AE/
The UMI sequence extracted by umi_tools doesn't seem to match the first 10 bases of the read.
Does someone have a suggestion what might be wrong?
Many thanks for any help!
Kind regards,
Nordin