adapters and barcode/UMI trimmed reads
Closed this issue · 2 comments
wanghlv commented
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
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
Thanks Neil! Yes, I realized that too, sorry for my blunder and your reminder!