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ref.yaml
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hg38:
salmon_index: ./ref_files/hg38/salmon_index/
STAR_index: ./ref_files/hg38/STAR_index/
rsem_index: ./ref_files/hg38/rsem_index/
gtf: ./ref_files/hg38/gencode.v29.primary_assembly.annotation_UCSC_names.gtf.gz
transformed_gtf: ./ref_files/hg38/hg38_gtf_full_table.txt.gz
tx2genename:
tx2geneid:
GPL: ./ref_files/GPL/
mm10:
salmon_index: ./ref_files/mm10/salmon_index/
STAR_index: ./ref_files/mm10/STAR_index/
rsem_index: ./ref_files/mm10/rsem_index/
gtf: ./ref_files/mm10/gencode.vM21.primary_assembly.annotation_UCSC_names.gtf.gz
transformed_gtf: ./ref_files/mm10/mm10_gtf_full_table.txt.gz
tx2genename: ./ref_files/mm10/tx2genename.tsv
tx2geneid: ./ref_files/mm10/tx2geneid.tsv
GPL: ./ref_files/GPL/
rn6:
salmon_index: ./ref_files/rn6/salmon_index/
STAR_index: ./ref_files/rn6/STAR_index/
rsem_index: ./ref_files/rn6/rsem_index/
gtf: ./ref_files/rn6/Rattus_norvegicus.Rnor_6.0.104.gtf.gz
transformed_gtf: ./ref_files/rn6/rn6_gtf_full_table.txt.gz
tx2genename:
tx2geneid:
GPL: ./ref_files/GPL/
# mm39:
# salmon_index: ./ref_files/mm39/salmon_index/
# STAR_index: ./ref_files/mm39/STAR_index
# gtf: ./ref_files/mm39/gencode.vM32.annotation.gtf.gz
# transformed_gtf: ./ref_files/mm39/mm39_gtf_full_table.txt.gz
# GPL: ./ref_files/GPL/
# rn7:
# salmon_index: ./ref_files/rn7/salmon_index/
# STAR_index: ./ref_files/rn7/STAR_index
# GPL: ./ref_files/GPL/