annotation-documents

[yurong-yang]

Could you please provide the following documents? Thank you!
#Only intron exon annotation
exon_intron_gtf:
mm10: "/groups/guttman/Peter/genomes/GRCm38.p6/GRCm38.p6.exon_intron.gtf.gz"
hg38: "/groups/guttman/Peter/genomes/GRCh38/GRCh38.exon_intron.gtf.gz"
#Annotation GTF of rmsk repeats and tRNAs used for featureCounts
anno_repeats_gtf:
mm10: "/groups/guttman/Peter/genomes/GRCm38.p6/repeats/mm10_rmskOutCurrent.gtf.gz"
hg38: "/groups/guttman/Peter/genomes/GRCh38/repeats/hg38_rmsk.gtf.gz"
#Repeat mask used for filtering DNA contacts
mask:
mm10: "/groups/guttman/Peter/genomes/GRCm38.p6/mm10_blacklist_rmsk.milliDivLessThan140.bed"
hg38: "/groups/guttman/Peter/genomes/GRCh38/hg38_blacklist_rmsk.milliDivLessThan140.bed"
#Other indexes
bowtie2_index:
mm10: "/groups/guttman/Peter/genomes/GRCm38.p6/GRCm38.p6"
hg38: "/groups/guttman/Peter/genomes/GRCh38/GRCh38"
psm44: "/groups/guttman/Peter/genomes/GRCm38.p6/snpsplit/CAST_EiJ_129S1_SvImJ_dual_hybrid.based_on_GRCm38_N-masked/GRCm38.p6_CAST_EiJ_129S1_SvImj_N-masked"
psm33: "/groups/guttman/Peter/genomes/GRCm38.p6/snpsplit/C57BL_6NJ_129S1_SvImJ_dual_hybrid.based_on_GRCm38_N-masked/GRCm38.p6_C57BL_6NJ_129S1_SvImJ_N-masked"
bowtie2_repeat_index:
mm10: "/groups/guttman/Peter/genomes/GRCm38.p6/repeats/mm_repetitive_sequences_20200109"
hg38: "/groups/guttman/Peter/genomes/GRCh38/repeats/Hs_repetitive_sequences_20200109"
hisat2_index:
mm10: "/groups/guttman/Peter/genomes/GRCm38.p6/GRCm38.p6"
hg38: "/groups/guttman/Peter/genomes/GRCh38/GRCh38"
hisat2_splice_sites:
mm10: "/groups/guttman/Peter/genomes/GRCm38.p6/Mus_musculus.GRCm38.95.ss"
hg38: "/groups/guttman/Peter/genomes/GRCh38/Homo_sapiens.GRCh38.97.ss"
snp_file:
psm33: "/groups/guttman/Peter/genomes/GRCm38.p6/snpsplit/all_129S1_SvImJ_SNPs_C57BL_6NJ_reference.based_on_GRCm38.txt"
psm44: "/groups/guttman/Peter/genomes/GRCm38.p6/snpsplit/all_129S1_SvImJ_SNPs_CAST_EiJ_reference.based_on_GRCm38.txt"
#Used for annotation of cluster file
snp_alleles:
psm33:
g1: "C57BL_6NJ"
g2: "129S1_SvImJ"
psm44:
g1: "CAST_EiJ"
g2: "129S1_SvImJ"