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Demultiplex horse+sill+speciesmix #22

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6 of 8 tasks
Cleiti opened this issue Jul 21, 2023 · 3 comments
Open
6 of 8 tasks

Demultiplex horse+sill+speciesmix #22

Cleiti opened this issue Jul 21, 2023 · 3 comments

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@Cleiti
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Cleiti commented Jul 21, 2023 •
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  • run demux häst upsplat
  • run demux häst oupsplat
  • run demux stats häst upsplat -> bekräfta
  • run demux stats häst oupsplat ->bekräfta
  • delete non-demux data to not take up space -> continue with demuxed
  • demux species_mix'
  • demux upSILL
  • demux oupSILL
@Cleiti
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Cleiti commented Jul 24, 2023 •
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oupSPLAT:

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

@Cleiti
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Cleiti commented Jul 24, 2023 •
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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
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Cleiti commented Jul 25, 2023

TODO: run the je data analys part of the pipeline

@Cleiti Cleiti changed the title Demultiplex new data Demultiplex horse+sill Aug 3, 2023
@Cleiti Cleiti changed the title Demultiplex horse+sill Demultiplex horse+sill+speciesmix Aug 3, 2023
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UpSPLAT @ SNP&SEQ
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@Cleiti