/1 and /2 suffixes in paired-end reads
See original GitHub issueHi, 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-pattern=XXXXXX
--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
--filter-cell-barcode
--whitelist=whitelist.txt
Read pairs do not match H3:1:CC9HDACXX:6:2209:1046:2076/1 != H3:1:CC9HDACXX:6:2209:1046:2076/2
Thanks,
Issue Analytics
- State:
- Created 5 years ago
- Comments:17 (13 by maintainers)
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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, notifications@github.com wrote:
This is now resolved in the master branch with option
--ignore-read-pair-suffixes
and will be available in the next release shortly