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Merge pull request #840 from maxplanck-ie/organism_yamls
Organism yamls
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| Original file line number | Diff line number | Diff line change |
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| blacklist_bed: /data/repository/organisms/GRCh38_gencode_40/akundaje/blacklist.bed | ||
| bowtie2_index: /data/repository/organisms/GRCh38_gencode_40/Indices/BowtieIndex/genome | ||
| bwa_index: /data/repository/organisms/GRCh38_gencode_40/Indices/BWAIndex/genome | ||
| bwameth_index: /data/repository/organisms/GRCh38_gencode_40/Indices/BWAmethIndex/genome.fa | ||
| extended_coding_regions_gtf: /data/repository/organisms/GRCh38_gencode_40/gencode/release-40/genes.slop.gtf | ||
| genes_bed: /data/repository/organisms/GRCh38_gencode_40/gencode/release-40/genes.bed | ||
| genes_gtf: /data/repository/organisms/GRCh38_gencode_40/gencode/release-40/genes.gtf | ||
| genome_2bit: /data/repository/organisms/GRCh38_gencode_40/genome_fasta/genome.2bit | ||
| genome_fasta: /data/repository/organisms/GRCh38_gencode_40/genome_fasta/genome.fa | ||
| genome_index: /data/repository/organisms/GRCh38_gencode_40/genome_fasta/genome.fa.fai | ||
| genome_size: 3105786285 | ||
| hisat2_index: /data/repository/organisms/GRCh38_gencode_40/Indices/HISAT2/genome | ||
| ignoreForNormalization: chrX chrY chrM GL000008.2 GL000009.2 GL000194.1 GL000195.1 | ||
| GL000205.2 GL000208.1 GL000213.1 GL000214.1 GL000216.2 GL000218.1 GL000219.1 GL000220.1 | ||
| GL000221.1 GL000224.1 GL000225.1 GL000226.1 KQ759759.1 ML143376.1 KN538364.1 ML143355.1 | ||
| ML143348.1 ML143347.1 ML143346.1 ML143352.1 KQ759762.1 ML143375.1 KQ031383.1 KN538369.1 | ||
| ML143342.1 ML143350.1 ML143362.1 JH159136.1 ML143357.1 ML143385.1 ML143378.1 ML143382.1 | ||
| ML143383.1 ML143384.1 JH159137.1 ML143356.1 ML143364.1 ML143365.1 KZ208923.1 KZ208924.1 | ||
| KQ031387.1 KV766195.1 KZ208916.1 ML143363.1 KN538360.1 KZ208920.1 KZ208906.1 KN196484.1 | ||
| KN196476.1 KQ983257.1 KN196479.1 KV575245.1 KZ208917.1 KZ208911.1 KN196473.1 KZ559108.1 | ||
| KN196487.1 KQ759760.1 KN196475.1 KV880766.1 KV880767.1 KQ090016.1 ML143374.1 KV880764.1 | ||
| KN538361.1 KN196474.1 ML143360.1 KZ559109.1 ML143359.1 KQ090022.1 KV766194.1 KN196478.1 | ||
| KZ559104.1 KN196480.1 ML143370.1 KQ090028.1 KN196483.1 KN196481.1 KN538363.1 KN538362.1 | ||
| KQ031385.1 KV766192.1 KQ031386.1 KQ031388.1 KN538365.1 KN538366.1 KN538367.1 ML143361.1 | ||
| KN538370.1 KN538373.1 KZ559113.1 KV880765.1 KV766196.1 KN538371.1 KQ031384.1 KN538372.1 | ||
| KQ090021.1 ML143371.1 KN196482.1 KZ559115.1 KZ208914.1 KZ208922.1 ML143373.1 ML143369.1 | ||
| ML143366.1 ML143367.1 ML143372.1 ML143380.1 ML143377.1 ML143345.1 KQ458386.1 ML143358.1 | ||
| KV575244.1 ML143381.1 KZ559100.1 ML143379.1 ML143354.1 ML143351.1 ML143353.1 ML143344.1 | ||
| ML143349.1 KZ208912.1 ML143341.1 KZ208915.1 KV880768.1 KN196472.1 GL383545.1 GL383546.1 | ||
| KI270824.1 KI270825.1 KQ090020.1 GL383547.1 KN538368.1 KI270826.1 KI270827.1 KZ559111.1 | ||
| KI270829.1 KI270830.1 KI270831.1 KI270832.1 KI270902.1 KI270903.1 KZ559110.1 KI270927.1 | ||
| GL877875.1 GL383549.1 GL383550.2 KQ090023.1 GL877876.1 GL383552.1 KI270904.1 GL383553.2 | ||
| KI270835.1 GL383551.1 KI270837.1 KI270833.1 KI270834.1 KI270836.1 KZ208918.1 KZ559112.1 | ||
| KI270838.1 KI270839.1 KI270840.1 KI270841.1 KI270842.1 KI270843.1 KQ090024.1 KQ090025.1 | ||
| KI270844.1 KI270845.1 KI270846.1 KI270847.1 KZ208919.1 ML143368.1 KI270852.1 KI270848.1 | ||
| GL383554.1 KI270906.1 GL383555.2 KI270851.1 KI270849.1 KI270905.1 KI270850.1 KQ031389.1 | ||
| KI270853.1 GL383556.1 GL383557.1 KI270855.1 KQ031390.1 KI270856.1 KQ090027.1 KQ090026.1 | ||
| KZ208921.1 KI270854.1 KI270909.1 KV766197.1 KZ559114.1 GL383563.3 KI270861.1 GL383564.2 | ||
| GL000258.2 KI270860.1 KI270907.1 KI270862.1 GL383565.1 KI270908.1 KV766198.1 KI270910.1 | ||
| GL383566.1 JH159146.1 JH159147.1 JH159148.1 KI270857.1 KI270858.1 KI270859.1 KZ559116.1 | ||
| GL383567.1 GL383568.1 GL383569.1 GL383570.1 GL383571.1 GL383572.1 KI270863.1 KI270864.1 | ||
| KQ458385.1 KI270912.1 KI270911.1 KV575254.1 KV575246.1 KV575256.1 KV575253.1 KV575252.1 | ||
| KV575255.1 KV575259.1 KI270917.1 KI270918.1 KI270919.1 KV575247.1 KV575248.1 KV575250.1 | ||
| KV575249.1 KV575257.1 KI270920.1 KI270921.1 KI270922.1 KI270923.1 KI270929.1 KI270930.1 | ||
| KI270931.1 KI270932.1 KI270933.1 KI270882.1 KI270883.1 KI270884.1 KI270885.1 KI270886.1 | ||
| KI270887.1 KI270888.1 KV575258.1 KV575251.1 KV575260.1 KI270889.1 KI270890.1 GL000209.2 | ||
| KI270891.1 KI270914.1 KI270915.1 KI270916.1 GL949746.1 GL949747.2 GL949748.2 GL949749.2 | ||
| GL949750.2 GL949751.2 GL949752.1 GL949753.2 GL383573.1 GL383574.1 GL383575.2 KI270866.1 | ||
| GL383576.1 KI270867.1 KI270865.1 KI270938.1 KI270868.1 KI270760.1 KI270762.1 GL383518.1 | ||
| KI270759.1 KI270766.1 GL383519.1 KI270761.1 KQ458382.1 GL383520.2 KI270763.1 KQ458383.1 | ||
| KI270765.1 KI270764.1 KQ983255.1 KQ458384.1 KV880763.1 KZ208904.1 KZ208905.1 KI270892.1 | ||
| GL383577.2 KI270869.1 KI270870.1 KI270871.1 GL383578.2 GL383579.2 GL383580.2 GL383581.2 | ||
| KI270872.1 KI270873.1 KI270874.1 GL383582.2 GL383583.2 KI270875.1 KI270876.1 KI270877.1 | ||
| KI270878.1 KI270879.1 KB663609.1 KI270928.1 KN196485.1 KN196486.1 KQ458387.1 KQ458388.1 | ||
| KQ759761.1 KI270769.1 KI270767.1 GL383521.1 KI270772.1 GL383522.1 KI270770.1 KI270893.1 | ||
| KI270894.1 GL582966.2 KI270773.1 KI270776.1 KI270768.1 KI270774.1 KI270771.1 KI270775.1 | ||
| KQ983256.1 KZ208907.1 KZ208908.1 JH636055.2 GL383526.1 KI270779.1 KI270777.1 KI270782.1 | ||
| KI270783.1 KI270778.1 KI270895.1 KZ208909.1 KI270780.1 KI270924.1 ML143343.1 KI270781.1 | ||
| KI270934.1 KZ559105.1 KI270935.1 KZ559101.1 KI270936.1 KZ559102.1 KI270937.1 KZ559103.1 | ||
| KI270784.1 KQ983258.1 KV766193.1 GL383527.1 KI270790.1 GL383528.1 KI270787.1 GL000257.2 | ||
| KI270785.1 KQ090013.1 KI270786.1 KI270788.1 KI270789.1 KI270896.1 KI270925.1 KQ090014.1 | ||
| KQ090015.1 GL383532.1 KI270897.1 GL383531.1 GL949742.1 GL339449.2 KI270795.1 KI270791.1 | ||
| GL383530.1 KI270898.1 KI270792.1 KI270796.1 KI270793.1 KI270794.1 KN196477.1 KV575243.1 | ||
| KZ208910.1 KQ090017.1 GL383533.1 KB021644.2 KI270797.1 KI270798.1 KI270799.1 KI270800.1 | ||
| KI270801.1 KI270802.1 KI270758.1 GL000250.2 GL000251.2 GL000252.2 GL000253.2 GL000254.2 | ||
| GL000255.2 GL000256.2 KI270804.1 KI270806.1 GL383534.2 KI270805.1 KI270899.1 KI270809.1 | ||
| KI270803.1 KI270807.1 KZ559106.1 KZ208913.1 KI270808.1 KI270811.1 KI270814.1 KI270810.1 | ||
| KI270812.1 KI270815.1 KI270813.1 KI270816.1 KI270818.1 KI270817.1 KI270900.1 KI270819.1 | ||
| KI270901.1 KI270820.1 KI270926.1 KZ559107.1 KI270821.1 KI270822.1 GL383539.1 GL383540.1 | ||
| GL383541.1 GL383542.1 KI270823.1 KQ090018.1 KQ090019.1 KI270880.1 KI270881.1 KI270913.1 | ||
| KV766199.1 KI270302.1 KI270303.1 KI270304.1 KI270305.1 KI270310.1 KI270311.1 KI270312.1 | ||
| KI270315.1 KI270316.1 KI270317.1 KI270320.1 KI270322.1 KI270329.1 KI270330.1 KI270333.1 | ||
| KI270334.1 KI270335.1 KI270336.1 KI270337.1 KI270338.1 KI270340.1 KI270362.1 KI270363.1 | ||
| KI270364.1 KI270366.1 KI270371.1 KI270372.1 KI270373.1 KI270374.1 KI270375.1 KI270376.1 | ||
| KI270378.1 KI270379.1 KI270381.1 KI270382.1 KI270383.1 KI270384.1 KI270385.1 KI270386.1 | ||
| KI270387.1 KI270388.1 KI270389.1 KI270390.1 KI270391.1 KI270392.1 KI270393.1 KI270394.1 | ||
| KI270395.1 KI270396.1 KI270411.1 KI270412.1 KI270414.1 KI270417.1 KI270418.1 KI270419.1 | ||
| KI270420.1 KI270422.1 KI270423.1 KI270424.1 KI270425.1 KI270429.1 KI270435.1 KI270438.1 | ||
| KI270442.1 KI270448.1 KI270465.1 KI270466.1 KI270467.1 KI270468.1 KI270507.1 KI270508.1 | ||
| KI270509.1 KI270510.1 KI270511.1 KI270512.1 KI270515.1 KI270516.1 KI270517.1 KI270518.1 | ||
| KI270519.1 KI270521.1 KI270522.1 KI270528.1 KI270529.1 KI270530.1 KI270538.1 KI270539.1 | ||
| KI270544.1 KI270548.1 KI270579.1 KI270580.1 KI270581.1 KI270582.1 KI270583.1 KI270584.1 | ||
| KI270587.1 KI270588.1 KI270589.1 KI270590.1 KI270591.1 KI270593.1 KI270706.1 KI270707.1 | ||
| KI270708.1 KI270709.1 KI270710.1 KI270711.1 KI270712.1 KI270713.1 KI270714.1 KI270715.1 | ||
| KI270716.1 KI270717.1 KI270718.1 KI270719.1 KI270720.1 KI270721.1 KI270722.1 KI270723.1 | ||
| KI270724.1 KI270725.1 KI270726.1 KI270727.1 KI270728.1 KI270729.1 KI270730.1 KI270731.1 | ||
| KI270732.1 KI270733.1 KI270734.1 KI270735.1 KI270736.1 KI270737.1 KI270738.1 KI270739.1 | ||
| KI270740.1 KI270741.1 KI270742.1 KI270743.1 KI270744.1 KI270745.1 KI270746.1 KI270747.1 | ||
| KI270748.1 KI270749.1 KI270750.1 KI270751.1 KI270752.1 KI270753.1 KI270754.1 KI270755.1 | ||
| KI270756.1 KI270757.1 | ||
| known_splicesites: /data/repository/organisms/GRCh38_gencode_40/gencode/release-40/HISAT2/genome.ss | ||
| rmsk_file: '' | ||
| star_index: /data/repository/organisms/GRCh38_gencode_40/Indices/STAR_2.7.10 | ||
| rmsk_file: /data/repository/organisms/GRCh38_gencode_40/repeatMasker/genome.fa.tbl |
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