TomSmithCGAT
commented
1 year ago Hi @robingarcia. To be clear, alevin is recommended over umi_tools to perform quantification from scRNA-Seq data. alevin was specifically developed for this purpose and works as an 'end-to-end' solution, e.g there's no separate 'extract' step equivalent with alevin. The upside of this is that it alevin provides more accurate quantification and runs much faster. The downside is that you can't operate on the output of any of the intermediate steps.
Looking at your cell barcode, I guess you might be working with 10X scRNAseq data using Chromium v2 barcodes. If so, you can include the --chromium flag and alevin will handle the barcodes appropriately. See here for alevin docs.
See also alevin-fry, for a more complete scRNA toolkit:
It is recommended to use Alevin instead of UMI tools. However, I cannot find the Extract feature from UMI-Tools in Alevin.
How would I write the following command in Alevin instead of UMI tools?
umi_tools extract --extract-method=regex \ --bc-pattern='(?P<cell_1>.{16})(?P<umi_1>.{10})' \ --stdin=Sample_S1_L004_R1_001.fastq.gz \ --stdout=proc_Sample_S1_L004_R1_001.fastq.gz \ --read2-in=Sample_S1_L004_R2_001.fastq.gz \ --read2-out=proc_Sample_S1_L004_R2_001.fastq.gz \ --whitelist=Sample_Whitelist_filt.csv \ --filtered-out=ext_Sample_S1_L004_R1_001.fastq.gz \ --filtered-out2=ext_Sample_S1_L004_R2_001.fastq.gzI am grateful for any hints.