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config.yaml
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config.yaml
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tmp_dir: "/fscratch/fanslerm"
gencodeValidEndsGTF: "/data/mayrc/data/mca/gff/gencode.vM25.mRNA_ends_found.gff3.gz"
utromeGTF: "/data/mayrc/data/mca/gff/utrome.e30.t5.gc25.pas3.f0.9999.w500.gtf.gz"
utromeKDX: "/data/mayrc/data/mca/kdx/utrome.e30.t5.gc25.pas3.f0.9999.w500.kdx"
utromeMerge: "/data/mayrc/data/mca/gff/utrome.e30.t5.gc25.pas3.f0.9999.w500.m200.tsv"
utromeIPA: "/data/mayrc/data/mca/gff/utrome.e30.t5.gc25.pas3.f0.9999.w500.ipa.tsv"
utromeBlacklist: "metadata/blacklist.utrome.genes.txt"
sce:
txs:
tmuris: "/data/mayrc/fanslerm/scutr-quant/data/sce/utrome_mm10_v2/tmuris.txs.Rds"
brain: "/data/mayrc/fanslerm/scutr-quant/data/sce/utrome_mm10_v2/ximerakis19.txs.Rds"
hspcs: "/data/mayrc/fanslerm/scutr-quant/data/sce/utrome_mm10_v2/dahlin18.txs.Rds"
mescs: "/data/mayrc/fanslerm/scutr-quant/data/sce/utrome_mm10_v2/guo19.txs.Rds"
genes:
tmuris: "/data/mayrc/fanslerm/scutr-quant/data/sce/utrome_mm10_v2/tmuris.genes.Rds"
brain: "/data/mayrc/fanslerm/scutr-quant/data/sce/utrome_mm10_v2/ximerakis19.genes.Rds"
hspcs: "/data/mayrc/fanslerm/scutr-quant/data/sce/utrome_mm10_v2/dahlin18.genes.Rds"
mescs: "/data/mayrc/fanslerm/scutr-quant/data/sce/utrome_mm10_v2/guo19.genes.Rds"