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Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow
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10x v2 filter part in config.yaml #100

Open YOU-k opened 4 years ago

YOU-k commented 4 years ago

Hi, I would like to run dropseqpipe for 10x v2 data. and i am not sure about what to be included in config.yaml. Here is what I have, FILTER: barcode-whitelist: '' 5-prime-smart-adapter: '' cell-barcode: start: 1 end: 16 UMI-barcode: start: 17 end: 26 cutadapt: adapters-file: R1: quality-filter: 30 maximum-Ns: 1 extra-params: '' R2: quality-filter: 30 minimum-adapters-overlap: 6 minimum-length: 15 extra-params: '' but I would get SyntaxError: Input and output files have to be specified as strings or lists of strings. i am not sure if empty cutadapt file is the reason for this. is there any suggestion for me? Thanks!

seb-mueller commented 4 years ago

An empty adapter file can well be the reason for it. Could you try with a non empty one? There are some in the template directory such as this one to try. Having said this, we should probably implement proper checks with meaningful error messages for this kind of thing. Please let us know if this was indeed the reason if you find out.

YOU-k commented 4 years ago

a randomly not empty one would work. but i have to check the stats for the percentage of trimmed sequences in case if some wanted sequences are trimmed accidentally.