annotate RNAseq files using info from file names

MEP-LINCS / knowledgeportal

Tracking issues related to https://www.synapse.org/mep_lincs

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Open kdaily opened 5 years ago

kdaily commented 5 years ago

example:

RNA171220LH_01_RNA_EGF_24_S18_L008

@danielderrick can you tell me what the fields are? I'm guessing EGF is a Ligand, 24 is a TimePoint?

danielderrick commented 5 years ago

@kdaily

For RNA171220LH_01_RNA_EGF_24_S18_L008, 01 = Replicate EGF = Ligand 24 = TimePoint

S18 = sample # from sequencing core (don't think this matters for annotation) L008 = lane # from sequencing core (same as above)

danielderrick commented 5 years ago

But there are some inconsistencies between what is in the filename fields and how we are annotating the samples:

Replicate is renamed: 02 becomes A, 03 = B, 04 = C, and 01 = D
Ligand: PBS is renamed to ctrl if TimePoint == 0
Ligand: IFNg renamed as IFNG
Ligand: TGFb renamed as TGFB
The sequencing core added a 5nM field to some, but not all, filenames - this field doesn't mean anything.

kdaily commented 5 years ago

Thank you! How does this translate into a sample name that is in one of the merged files?

kdaily commented 5 years ago

Nevermind - I see that you have some metadata files here. Can push these to annotations: