UMI-tools Extract not working

Hi, what is causing the error message here:

Traceback (most recent call last):
  File "/usr/local/tools/_conda/envs/__umi_tools@1.1.2/bin/umi_tools", line 11, in <module>
  File "/usr/local/tools/_conda/envs/__umi_tools@1.1.2/lib/python3.8/site-packages/umi_tools/", line 61, in main
  File "/usr/local/tools/_conda/envs/__umi_tools@1.1.2/lib/python3.8/site-packages/umi_tools/", line 477, in main
    reads = ReadExtractor(read1, read2)
  File "/usr/local/tools/_conda/envs/__umi_tools@1.1.2/lib/python3.8/site-packages/umi_tools/", line 544, in __call__
    raise ValueError('Read sequence: %s is shorter than pattern: %s' % (
ValueError: Read sequence: ACGC is shorter than pattern: NNNXXXXNN

Hi @biostaring,
it seems that your FASTQ file contains reads whose length is shorter than the barcode pattern; in order to solve it, you need to filter your reads by length >=10, by using for example cutadapt.


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