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If / characters are in the read names, then the pipeline will fail at the dedup step. This is caused, however, by STAR truncating read names based on the / character. This removes the UMI information which was added earlier in the pipeline, causing the dedup step to fail.
Steps to reproduce
Steps to reproduce the behaviour:
Running the pipeline with reads with a / in the read name. Example
Expected behaviour
Either a verbose error message saying that the reads are incompatible, or automatic removal or replacement of the / characters.
The text was updated successfully, but these errors were encountered:
Interestingly, when there's a space in the read it works correctly:
# initial format
@ERR039787.1 HWI-EAS202_223:6:1:37:2026/1
# format after move_umi
@ERR039787.2_GTTCCAC HWI-EAS202_223:6:1:41:30/1
# format after STAR mapping
ERR039788.1477620_GAAGCCC
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Description of the bug
If
/
characters are in the read names, then the pipeline will fail at thededup
step. This is caused, however, by STAR truncating read names based on the/
character. This removes the UMI information which was added earlier in the pipeline, causing thededup
step to fail.Steps to reproduce
Steps to reproduce the behaviour:
Running the pipeline with reads with a
/
in the read name. ExampleExpected behaviour
Either a verbose error message saying that the reads are incompatible, or automatic removal or replacement of the
/
characters.The text was updated successfully, but these errors were encountered: