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Merge pull request #963 from maxplanck-ie/mm39_ref
correct paths in pre-shipped MM39 ref
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,23 +1,23 @@ | ||
| blacklist_bed: '' | ||
| bowtie2_index: /data/repository/organisms/GRCm39_ensembl_106/Indices/BowtieIndex/genome | ||
| bwa_index: /data/repository/organisms/GRCm39_ensembl_106/Indices/BWAIndex/genome | ||
| bwa_mem2_index: /data/repository/organisms/GRCm39_ensembl_106/Indices/BWAMEM2Index/genome | ||
| bwameth_index: /data/repository/organisms/GRCm39_ensembl_106/Indices/BWAmethIndex/genome.fa | ||
| bwameth2_index: /data/repository/organisms/GRCm39_ensembl_106/Indices/BWA2methIndex/genome.fa | ||
| extended_coding_regions_gtf: /data/repository/organisms/GRCm39_ensembl_106/ensembl/release-106/genes.slop.gtf | ||
| genes_bed: /data/repository/organisms/GRCm39_ensembl_106/ensembl/release-106/genes.bed | ||
| genes_gtf: /data/repository/organisms/GRCm39_ensembl_106/ensembl/release-106/genes.gtf | ||
| genome_2bit: /data/repository/organisms/GRCm39_ensembl_106/genome_fasta/genome.2bit | ||
| genome_fasta: /data/repository/organisms/GRCm39_ensembl_106/genome_fasta/genome.fa | ||
| genome_index: /data/repository/organisms/GRCm39_ensembl_106/genome_fasta/genome.fa.fai | ||
| genome_size: 2654621783 | ||
| genome_fasta: "/data/repository/organisms/GRCm39_ensembl_106/genome_fasta/genome.fa" | ||
| genome_index: "/data/repository/organisms/GRCm39_ensembl_106/genome_fasta/genome.fa.fai" | ||
| genome_2bit: "/data/repository/organisms/GRCm39_ensembl_106/genome_fasta/genome.2bit" | ||
| bowtie2_index: "/data/repository/organisms/GRCm39_ensembl_106/Indices/BowtieIndex/genome" | ||
| hisat2_index: "/data/repository/organisms/GRCm39_ensembl_106/Indices/HISAT2Index/genome" | ||
| bwa_index: "/data/repository/organisms/GRCm39_ensembl_106/Indices/BWAindex/genome.fa" | ||
| bwa_mem2_index: "/data/repository/organisms/GRCm39_ensembl_106/Indices/BWAMEM2Index/genome" | ||
| bwameth_index: "/data/repository/organisms/GRCm39_ensembl_106/Indices/BWAmethIndex/genome.fa" | ||
| bwameth2_index: | ||
| known_splicesites: "/data/repository/organisms/GRCm39_ensembl_106/ensembl/release-106/HISAT2/genome.ss" | ||
| star_index: "/data/repository/organisms/GRCm39_ensembl_106/Indices/STARIndex/2.7.10a/" | ||
| genes_bed: "/data/repository/organisms/GRCm39_ensembl_106/ensembl/release-106/genes.bed" | ||
| genes_gtf: "/data/repository/organisms/GRCm39_ensembl_106/ensembl/release-106/genes.gtf" | ||
| extended_coding_regions_gtf: "/data/repository/organisms/GRCm39_ensembl_106/ensembl/release-106/genes.slop.gtf" | ||
| blacklist_bed: "" | ||
| ignoreForNormalization: "MT X Y JH584299.1 GL456233.2 JH584301.1 GL456211.1 GL456221.1 | ||
| hisat2_index: /data/repository/organisms/GRCm39_ensembl_106/Indices/HISAT2/genome | ||
| ignoreForNormalization: MT X Y JH584299.1 GL456233.2 JH584301.1 GL456211.1 GL456221.1 | ||
| JH584297.1 JH584296.1 GL456354.1 JH584298.1 JH584300.1 GL456219.1 GL456210.1 JH584303.1 | ||
| JH584302.1 GL456212.1 JH584304.1 GL456379.1 GL456366.1 GL456367.1 GL456239.1 GL456383.1 | ||
| GL456385.1 GL456360.1 GL456378.1 MU069435.1 GL456389.1 GL456372.1 GL456370.1 GL456381.1 | ||
| GL456387.1 GL456390.1 GL456394.1 GL456392.1 GL456382.1 GL456359.1 GL456396.1 GL456368.1 | ||
| MU069434.1 JH584295.1" | ||
| rmsk_file: '/data/repository/organisms/GRCm39_ensembl_release_106/repeatMasker/genome.fa.tbl' | ||
| MU069434.1 JH584295.1 | ||
| known_splicesites: /data/repository/organisms/GRCm39_ensembl_106/ensembl/release-106/HISAT2/genome.ss | ||
| rmsk_file: /data/repository/organisms/GRCm39_ensembl_106/repeatMasker/genome.fa.tbl | ||
| star_index: /data/repository/organisms/GRCm39_ensembl_106/Indices/STAR_2.7.10 |