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marcelm, fileadapterendrfasta, cutadapt, pairs, demultiplexing, sign, written, issue, discarduntrimmed, discarding, untrimmed, tmfq, tmpfq, navigation, pull, requests, actions, security, closed, reads, report, correctly, testdnamefq, pairadapters, testdpnamefq, testdcnamenamefq, commented, owner, fix, github, labels, projects, milestone, footer, skip, content, menu, product, solutions, resources, open, source, enterprise, pricing, search, jump, public, notifications, fork, star,

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test_dc_{name1}_{name2}_1 test_dc_{name1}_{name2}_2 demultiplexing paired-end reads pairs written marcelm closed fasta --discard-untrimmed combinatorial dual indexes comment metadata assignees pair-adapters discard-untrimmed cutadapt 5b801c1 sign demultiplexed correctly trimming adapter command line investigate closer fix reported number normal demultiplexer ve found chlige added assigned labels labels projects projects milestone milestone relationships fq tm fq tm_p github demultiplexing txt reads fasta }_1 }_2 fq sign skip jump python 3 r1 r2 report pass filter outputted file /adapter_5end_r1 /adapter_5end_r2 test_d_{ test_d

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      context:https://schema.org
      headline:pairs written is 0 when demultiplexing and discarding untrimmed
      articleBody:cutadapt 2.10 with Python 3.8.6 When demultiplexing paired-end reads and trimming adapter from both R1 and R2, and discarding untrimmed read pairs, the "Pairs written" in the report is always 0, although some reads do pass the filter and are outputted and demultiplexed correctly. The command line is like: ```bash cutadapt -g file:./adapter_5end_R1.fasta -G file:./adapter_5end_R2.fasta --discard-untrimmed -o test_d_{name}_1.fq -p test_d_{name}_2.fq tm.fq tm_p.fq >! test_d.txt ``` This also occurs when using `--pair-adapters`: ```bash cutadapt -g file:./adapter_5end_R1.fasta -G file:./adapter_5end_R2.fasta --pair-adapters --discard-untrimmed -o test_dp_{name}_1.fq -p test_dp_{name}_2.fq tm.fq tm_p.fq >! test_dp.txt ``` However, when demultiplexing with combinatorial dual indexes, it reports the pairs written correctly ``` bash cutadapt -g file:./adapter_5end_R1.fasta -G file:./adapter_5end_R2.fasta --discard-untrimmed -o test_dc_{name1}_{name2}_1.fq -p test_dc_{name1}_{name2}_2.fq tm.fq tm_p.fq >! test_dc.txt ```
      author:
         url:https://github.com/qifei9
         type:Person
         name:qifei9
      datePublished:2020-10-26T18:22:48.000Z
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      url:https://github.com/487/cutadapt/issues/487
      context:https://schema.org
      headline:pairs written is 0 when demultiplexing and discarding untrimmed
      articleBody:cutadapt 2.10 with Python 3.8.6 When demultiplexing paired-end reads and trimming adapter from both R1 and R2, and discarding untrimmed read pairs, the "Pairs written" in the report is always 0, although some reads do pass the filter and are outputted and demultiplexed correctly. The command line is like: ```bash cutadapt -g file:./adapter_5end_R1.fasta -G file:./adapter_5end_R2.fasta --discard-untrimmed -o test_d_{name}_1.fq -p test_d_{name}_2.fq tm.fq tm_p.fq >! test_d.txt ``` This also occurs when using `--pair-adapters`: ```bash cutadapt -g file:./adapter_5end_R1.fasta -G file:./adapter_5end_R2.fasta --pair-adapters --discard-untrimmed -o test_dp_{name}_1.fq -p test_dp_{name}_2.fq tm.fq tm_p.fq >! test_dp.txt ``` However, when demultiplexing with combinatorial dual indexes, it reports the pairs written correctly ``` bash cutadapt -g file:./adapter_5end_R1.fasta -G file:./adapter_5end_R2.fasta --discard-untrimmed -o test_dc_{name1}_{name2}_1.fq -p test_dc_{name1}_{name2}_2.fq tm.fq tm_p.fq >! test_dc.txt ```
      author:
         url:https://github.com/qifei9
         type:Person
         name:qifei9
      datePublished:2020-10-26T18:22:48.000Z
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      url:https://github.com/487/cutadapt/issues/487
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      name:qifei9
      url:https://github.com/qifei9
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