Demultiplex horse+sill+speciesmix

Cleiti / UpSPLAT

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Demultiplex horse+sill+speciesmix #22

Open Cleiti opened 1 year ago

Cleiti commented 1 year ago

[x] run demux häst upsplat
[x] run demux häst oupsplat
[x] run demux stats häst upsplat -> bekräfta
[x] run demux stats häst oupsplat ->bekräfta
[x] delete non-demux data to not take up space -> continue with demuxed
[x] demux species_mix'
[ ] demux upSILL
[ ] demux oupSILL

Cleiti commented 1 year ago

oupSPLAT:

[x] skapa mapp med all behövd kod
[x] flytta upp plate_specs
[x] byta plate_specs to csv (have code for it somewhere?)
[x] modifiera all kod förutom barcodeparse for this run
[x] Modifiera barcode-parsing code for oupSPLAT, 6bp lång + kolla rött på xlsx
[x] runit

Cleiti commented 1 year ago

CHANGES for horse-genomes in prep_sarek.py: --genome changed to specified string path for --fasta and --fasta_fai (index) (why? iGenomes default only had -2 version of wanted genome (not -3), a file is safebet)

Cleiti commented 1 year ago

TODO: run the je data analys part of the pipeline