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/1 and /2 suffixes in paired-end reads

See original GitHub issue

Hi, Can umi-tools analyze paired-end reads with /1 and /2 suffixes instead of 1:N and 2:N ?

trying with v0.5.5 and get the error message below with umi-tools extract:

umi-tools extract 
--bc-pattern2 CCCCCCNNNN 
--stdin H619_RG_C000QSP_6_1_CC9HDACXX_S0_L001_R1_001.fastq.gz 
--stdout H619_RG_C000QSP_6_1_CC9HDACXX_S0_L001_R1_001_extracted.fastq.gz 
--read2-in H619_RG_C000QSP_6_1_CC9HDACXX_S0_L001_R2_001.fastq.gz 
--read2-out H619_RG_C000QSP_6_1_CC9HDACXX_S0_L001_R2_001_extracted.fastq.gz 

Read pairs do not match H3:1:CC9HDACXX:6:2209:1046:2076/1 != H3:1:CC9HDACXX:6:2209:1046:2076/2


Issue Analytics

  • State:closed
  • Created 5 years ago
  • Comments:17 (13 by maintainers)

github_iconTop GitHub Comments

IanSudberycommented, Mar 15, 2019

I wonder if instead of having two options we should just have one, that takes the delimiter and only uses it if one is provided. In fact I reckon that we already have a default, which is space.

On Fri, 15 Mar 2019, 4:16 pm Tom Smith, wrote:

Great. Let me know when you’ve run the alignment and deduplication and confirmed this all works OK. Then I’ll merge this into the master and close the issue.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread .

TomSmithCGATcommented, Sep 14, 2020

This is now resolved in the master branch with option --ignore-read-pair-suffixes and will be available in the next release shortly

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