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mritchielab / FLAMES

A framework for performing single-cell and bulk read full-length analysis of mutations and splicing.
https://mritchielab.github.io/FLAMES/
GNU General Public License v3.0
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Running Multisample pipeline #11

Closed mcortes-lopez closed 7 months ago

mcortes-lopez commented 1 year ago

Hi,

I am trying to run the multisample pipeline for 3 sc datasets, however I am not sure how to provide the barcodes for each sample separately. I tried it as vectors with the path to each barcode file but that does not seem to work. Can I, otherwise, run the pipeline from the aligned bam files? So far I tried this second option by providing a list of bam files, but the problem was that when aligning the fastq files (provided in a list) to the transcriptome, the barcode was lost and consequently no isoform quantification was possible. Do I need perhaps to recreate the fastq files from the bam files after align to the transcriptome? I just want to have all these samples, which I already run individually, quantified in the same transcriptome. Thanks.

ChangqingW commented 1 year ago

You could use find_barcode function individually on each sample, and then run the pipeline with the demultiplexed reads, setting match_barcode to FALSE. We will add the support for vector of barcode files soon.