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bcl2fastq

Hi everybody I have run this code with data sheat. But I just got two fastq file Undetermined_S0_R1_001.fastq.gz Undetermined_S0_R2 _001.fastq.gz. Is there a reason why the other sample didn't generate?

bcl2fastq -R /crex/proj/naiss2023-22-1174/Masomeh \
          -i /crex/proj/naiss2023-22-1174/Masomeh/BaseCalls/ \
          -o /crex/proj/naiss2023-22-1174/Masomeh/BaseCalls/ \
          --interop-dir /crex/proj/naiss2023-22-1174/Masomeh/InterOp/ \
          --stats-dir /crex/proj/naiss2023-22-1174/Masomeh/BaseCalls/Stats/ \
          --reports-dir /crex/proj/naiss2023-22-1174/Masomeh/BaseCalls/Reports/ \
          --sample-sheet /crex/proj/naiss2023-22-1174/Masomeh/ATAC_csv_file.csv \
          -r 4 -p 40 -w 4 \
          --minimum-trimmed-read-length 35 --mask-short-adapter-reads 22 \
          --adapter-stringency 0.9 --ignore-missing-bcls --ignore-missing-filter \
          --ignore-missing-positions --no-lane-splitting \
          --include-non-PF-clusters YES![enter image description here][1]


This the data sheat that i have used 


  [1]: /media/images/e936af99-6ac8-41aa-8055-c2204b71
  [2]: /media/images/6566c766-3495-4f10-a624-178c6f5b
bcl2fstq
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written by daffodil • daffodil

Problem is more than likely in your samplesheet. How many cycles was this run for and for what sequencer?

Run some code I have here on the "Undetermined" files and check the indexes that sequencer sees (not what you think they should be): Demultiplexing reads with index present in the labels

You also did not attach the images correctly though they are probably not critical.

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written by GenoMax GenoMax

the sequencer is nextseq550. I have change sample sheet but again I got the same result. Whould you mind please let me know what should I. have to do?

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written by daffodil • daffodil

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