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MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
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Accomodating fastq file names from other sequencers (BGISEQ) #19

Closed methylnick closed 6 years ago

methylnick commented 6 years ago

It appears with BGI, they have their own result output structure. Which has some implications with RNASik and how it handles such files.

please see this path: /mnt/cephfs/scratch/nick.wong/alison.anderson/cdts-wh.genomics.cn/F18FTSAPHT0121_HUMxcaE/Clean

Differences are, each sample is a folder. Within each folder is the fastq file name which is a different structure than normal Illumina data.

CL100059708_L2_WHHUMxcaEAABRAAPEI-543_1.fq.gz

_1 is the read id 543 is the sample number the preceding characters are the machine and flowcell it would seem.

serine commented 6 years ago

@methylnick sorry taking it a while to get back to you. RNAsik should handle this fine. I might have made some improvements in the last couple of month, so best to grab latest version.

Use these options when running RNAsik

-pairIds "_1,_2" -extn "fq.gz"

Let me know how it goes

Cheers

serine commented 6 years ago

@methylnick going to close this issue as I think it should all work and not actual bug/problem with the code. Feel free to reopen if needed.

Cheers