Merge Undetermined.fq files from multiple sequencing runs (BCL) prior to sample-demuxxing.

odomlab2 / sci-rocket

Snakemake workflow for (pre-)processing sci-RNA-seq3 data

MIT License

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Merge Undetermined.fq files from multiple sequencing runs (BCL) prior to sample-demuxxing. #13

Closed J0bbie closed 10 months ago

J0bbie commented 11 months ago

If the same sequencing_name + sample_name is defined but from different path_bcl (sequencing runs):

Merge Undetermined.fq (after bcl2fastq) of path_bcl
Proceed with demuxxing on this merged file.

J0bbie commented 10 months ago

Multiple sequencing runs (different path_bcl but same experiment_name) are now merged. bcl2fastq is performed per sequencing run and the resulting Undetermined_S0_R1_001.fastq.gz and Undetermined_S0_R2_001.fastq.gz are merged (cat) prior to downstream sample demuxxing.