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Add option to set the delimiter between the read name and the UMI #421

Merged
merged 1 commit into from
Mar 22, 2023
Merged

Add option to set the delimiter between the read name and the UMI #421

merged 1 commit into from
Mar 22, 2023

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Redmar-van-den-Berg
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@Redmar-van-den-Berg Redmar-van-den-Berg commented Aug 4, 2022 •
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This allows fastp to match the behaviour of UMI-Tools, which uses (and requires) an underscore between the read name and the UMI.

e.g.

$ fastp -i R1.fq -o out.R1.fq --umi --umi_loc=read1 --umi_len=8 --umi_delim=_
$ head out.R1.fq
@AS500713:64:HFKJJBGXY:1:11101:17113:1101_TACAAAAT 1:A:0:TATAGCCT+GTTTCTTA
GCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT
+
EE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEECFE####EEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE
@AS500713:64:HFKJJBGXY:1:11101:1675:1101_TAGGAGGC 1:A:0:TATAGCCT+GACCCCCA
TTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAATTTTTAAACCCAGGCAGCTTCCTGGCAGTGACATTTGGAGCATCAAAGTGGTAAATAAAATTTCATTTACATTAATAT
+
EEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAAA/E###6E/6//6<EAAEEE/EEEA/EA/EEEEEE/<<EEEE//A/EE<AEEEEE/</AA</E<AAAE/E<E/
@AS500713:64:HFKJJBGXY:1:11101:17113:1101_TACAAAAT 1:A:0:TATAGCCT+GTTTCTTA

@Redmar-van-den-Berg
Add option to set the delimiter between the read name and the UMI
a823302 
This allows fastp to match the behaviour of UMI-Tools, which uses an
underscore between the read name and the UMI.
@sfchen sfchen merged commit f6c5cda into OpenGene:master Mar 22, 2023
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@Redmar-van-den-Berg @sfchen