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chris-mcginnis-ucsf / MULTI-seq

R implementation of MULTI-seq sample classification workflow
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MULTIseq.preProcess #2

Closed lk9-lnx closed 5 years ago

lk9-lnx commented 5 years ago

I'm using MULTI-seq on hashing data. I'm getting the following error when I tried to use MULTIseq.preProcess function. Is there an issue?

Error in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord, : solving row 1: 'allow.nonnarrowing' is FALSE and the supplied end (28) is > refwidth

lk9-lnx commented 5 years ago

What does 'good.bars' refer to in the tutorial?

chris-mcginnis-ucsf commented 5 years ago

Apologies for the delayed response.

This error is likely caused because your sequencing settings only took the first 26 bases of R1, and the default chemistry argument previously looked at the first 28 bases. I've adjusted the arguments to make this more flexible, and have also included a more specific description of 'good.bars' in the ReadMe.

Chris

RM-SCB commented 5 years ago

I got into the same confusion, but then found this issue and realised 26 was the number to use. Might be worth either editing the tutorial with 26 instead of 28 or adding a line to flag it so that people not careful enough like me make sure to edit this! :)

chris-mcginnis-ucsf commented 5 years ago

The 10x V3 reagents have CB=16bp and UMI=12bp, whereas 10x V2 reagents have CB=16bp and UMI=10bp. Since V2 reagents are being phased out, I think it makes sense to keep the current default arguments. But I like the idea of adding some sort of flag!

uni987 commented 3 months ago

What is a nice job! I have been trying to use three cellIDs label fragments to improve its stability, however, how can I adjust the arguments to make it. I am looking forward to your prompt reply!! Thanks like this【readTable <- MULTIseq.preProcess(R1 = '/path/to/R1.fastq.gz', R2 = '/path/to/R2.fastq.gz', cellIDs = cell.id.vec, cell=c(1,16), umi=c(17,28), tag=c(1,8))】