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adapters and barcode/UMI trimmed reads #117

Closed wanghlv closed 4 months ago

wanghlv commented 4 months ago

Ask away!

Hi Thanks for updating the workflow so many major nice changes! I'm wondering if the trimmed reads after removal of adapter 1/2 and barcodes and umi were in the output folder? I'd like to run the reads through SQANTI3. https://github.com/ConesaLab/SQANTI3. Thanks a lot!!

nrhorner commented 4 months ago

Hi @wanghlv

The trimmed fastq are not output by the workflow, but the BAM files generated from mapping those trimmed reads can be found at -out_dir/<sample_id>/tagged.bam. You will be able to extract fastq from these with, for example, samtools fastq.

Thanks,

Neil

wanghlv commented 4 months ago

Thanks Neil! Yes, I realized that too, sorry for my blunder and your reminder!