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Clarified Selecting the representative read documentation
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A user queried the use of quality in which read is kept upon
deduplication (#261)

> your selection procedure does not seem to take into
> account read sequencing quality (only mapping quality).
>
> In other words, if 2 reads have the same high score
> mapping quality (i.e. unique mappers), one being long and
> with good base scores, the other short with errors, it will
> select randomly among these, too, right?

The response was:

> Yes, that's correct.

Updated umi-tools/dedup.py "Selecting the representative read" comment
section to clarify that the read quality is not used.
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mikej888 committed Oct 31, 2019
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5 changes: 4 additions & 1 deletion umi_tools/dedup.py
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Expand Up @@ -23,7 +23,10 @@
1. The read with the lowest number of mapping coordinates (see
``--multimapping-detection-method`` option)
2. The read with the highest mapping quality
2. The read with the highest mapping quality. Note that this is not
the read sequencing quality and that if two reads have the same
mapping quality then one will be picked at random regardless of the
read quality.
Otherwise a read is chosen at random.
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