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step3/star-alignment-snippet

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• 35f356dd33 Use BAM files for htseq-count. master Hylke C. Donker 2021-03-17 17:06:02 +0100
• 4b449ded08 Bug fix in trimmomatic paired-end flag. Hylke C. Donker 2021-03-10 13:45:06 +0100
• 1c42a61e48 Updated htseq-count with extra comments. Hylke C. Donker 2021-02-25 16:59:57 +0100
• e852072235 Added htseq-count snippet + updated STAR snippet indicating prebuilt genome index. Hylke C. Donker 2021-02-25 12:40:17 +0100
• 4443b3c2a9 Merge pull request 'Comments to umi deduplication script' (#8) from s3970582/system_genetics:master into master T. Karp 2021-02-23 15:24:45 +0100
• d4016b44b6 Added comments to umi deduplication 1740213937118722974/tmp_refs/heads/master 1740213937118722974/master 1739086503717921260/tmp_refs/heads/master 1739086503717921260/master 1738649005771429105/tmp_refs/heads/master 1738649005771429105/master 1737269074049139600/tmp_refs/heads/master 1737269074049139600/master 1736436904841659071/tmp_refs/heads/master 1736436904841659071/master 1734162584524091577/tmp_refs/heads/master 1734162584524091577/master 1733813225530429378/tmp_refs/heads/master 1733813225530429378/master 1733813211761056143/tmp_refs/heads/master 1733813211761056143/master 1733794807281651351/tmp_refs/heads/master 1733794807281651351/master 1733664125807735973/tmp_refs/heads/master 1733664125807735973/master 1733593943358998501/tmp_refs/heads/master 1733593943358998501/master 1733588244499469512/tmp_refs/heads/master 1733588244499469512/master 1733560960782587708/tmp_refs/heads/master 1733560960782587708/master 1733502921260259976/tmp_refs/heads/master 1733502921260259976/master 1733386716813899627/tmp_refs/heads/master 1733386716813899627/master 1733382032983705099/tmp_refs/heads/master 1733382032983705099/master 1733320080106009035/tmp_refs/heads/master 1733320080106009035/master 1733304963289345632/tmp_refs/heads/master 1733304963289345632/master 1733257807004396712/tmp_refs/heads/master 1733257807004396712/master 1733256529549439979/tmp_refs/heads/master 1733256529549439979/master 1732932495063065883/tmp_refs/heads/master 1732932495063065883/master 1732904252637802791/tmp_refs/heads/master 1732904252637802791/master 1732895790320246688/tmp_refs/heads/master 1732895790320246688/master 1732878410685447255/tmp_refs/heads/master 1732878410685447255/master 1732844497797828654/tmp_refs/heads/master 1732844497797828654/master 1723872735646101635/tmp_refs/heads/master 1723872735646101635/master 1723709199225828497/tmp_refs/heads/master 1723709199225828497/master 1723708980024060773/tmp_refs/heads/master 1723708980024060773/master 1723647074694063103/tmp_refs/heads/master 1723647074694063103/master 1722553048751759861/tmp_refs/heads/master 1722553048751759861/master 1722552725508114254/tmp_refs/heads/master 1722552725508114254/master 1717369700216210198/tmp_refs/heads/master 1717369700216210198/master 1717369685867567443/tmp_refs/heads/master 1717369685867567443/master 1708658534441888972/tmp_refs/heads/master 1708658534441888972/master TatiKarp 2021-02-23 15:18:35 +0100
• f58dfdaad6 Merge pull request 'Pulling from system_genetic to my repository' (#1) from GRIAC/system_genetics:master into master T. Karp 2021-02-23 15:08:28 +0100
• 3e02b07f83 Merge pull request 'Pulling from system_genetics' (#1) from GRIAC/system_genetics:master into master 1695428793532999574/tmp_refs/heads/master J.v.N. 2021-02-23 15:08:25 +0100
• 55658e204f Merge pull request 'Made snippet input- and output files more harmonised.' (#6) from feature/harmonised-steps into master H.C. Donker 2021-02-23 09:17:16 +0100
• f93596dd87 Made snippet input- and output files more harmonised. Hylke C. Donker 2021-02-22 13:18:18 +0100
• e3c88c059f added description of general files 1740191300180000725/tmp_refs/heads/master 1740191300180000725/master 1739829944832744299/tmp_refs/heads/master 1739829944832744299/master 1739778492054943331/tmp_refs/heads/master 1739778492054943331/master 1739641911223023316/tmp_refs/heads/master 1739641911223023316/master 1739570464955945510/tmp_refs/heads/master 1739570464955945510/master 1739551376793378519/tmp_refs/heads/master 1739551376793378519/master 1739458623754562696/tmp_refs/heads/master 1739458623754562696/master 1739420401745974672/tmp_refs/heads/master 1739420401745974672/master 1739363240124161817/tmp_refs/heads/master 1739363240124161817/master 1739293818162511175/tmp_refs/heads/master 1739293818162511175/master 1739258315967794007/tmp_refs/heads/master 1739258315967794007/master 1739174050906496607/tmp_refs/heads/master 1739174050906496607/master 1739127933721039354/tmp_refs/heads/master 1739127933721039354/master 1738900673316858762/tmp_refs/heads/master 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1717336134258022384/tmp_refs/heads/master 1717336134258022384/master 1717333393281465163/tmp_refs/heads/master 1717333393281465163/master 1717330413281948226/tmp_refs/heads/master 1717330413281948226/master 1717206663108497732/tmp_refs/heads/master 1717206663108497732/master 1716564334646516072/tmp_refs/heads/master 1716564334646516072/master 1713164145493027856/tmp_refs/heads/master 1713164145493027856/master 1678002452350328520/tmp_refs/heads/master 1678002452350328520/master Rene Bults 2021-02-22 15:20:41 +0100
• a2bc313515 Simple snippet on running MultiQC to collate FastQC results M. Berg 2021-02-22 14:52:54 +0100
• 981a983dd5 Merge pull request 'UMI deduplication script from Victor' (#3) from s3970582/system_genetics:master into master T. Karp 2021-02-15 17:44:30 +0100
• c05d3f7868 Added description and some comments for UMi deduplication TatiKarp 2021-02-15 17:18:48 +0100
• 59f1b425b1 Merge pull request 'Small snippet that generates a genome index and aligns the RNAseq reads.' (#2) from step3/star-alignment-snippet into master J.v.N. 2021-02-15 17:09:28 +0100
• 65d7193848 Merge branch 'master' into step3/star-alignment-snippet step3/star-alignment-snippet J.v.N. 2021-02-15 17:08:31 +0100
• cba83716c8 Merge pull request 'Trimmomatic update (simplified)' (#5) from P300299/system_genetics:master into master J.v.N. 2021-02-15 17:06:31 +0100
• 6cf40804c4 adapter comments Jos van Nijnatten 2021-02-15 17:03:34 +0100
• 51abdcdb26 Trimmomatic update (simplified) Jos van Nijnatten 2021-02-15 16:48:39 +0100
• e2206cbc39 Merge pull request 'FastQC, Trimming, Overall QC (initial)' (#1) from P300299/system_genetics:master into master J.v.N. 2021-02-15 16:20:20 +0100
• 4c52527340 Merge branch 'master' into master J.v.N. 2021-02-15 16:18:28 +0100
• 1110d00e8c added fastQC code snippet (.pl and .sh scripts) Rene Bults 2021-02-15 15:54:21 +0100
• 170a001729 Count reads in X and Y chromosome. Jos van Nijnatten 2021-02-15 12:54:31 +0100
• 4b61c099f6 Update 'rnaseq/step2_trim/snippet.sh' C. Qi 2021-02-13 19:13:13 +0100
• 96a1e59daf Add 'rnaseq/step5_count/snippet_counts' 1740146774876837647/tmp_refs/heads/p280381-featureCounts-1 1740146774876837647/p280381-featureCounts-1 1740097379154192540/tmp_refs/heads/p280381-featureCounts-1 1740097379154192540/p280381-featureCounts-1 1739718185639100918/tmp_refs/heads/p280381-featureCounts-1 1739718185639100918/p280381-featureCounts-1 1739616417500634248/tmp_refs/heads/p280381-featureCounts-1 1739616417500634248/p280381-featureCounts-1 1739540372030183523/tmp_refs/heads/p280381-featureCounts-1 1739540372030183523/p280381-featureCounts-1 1739259196412031631/tmp_refs/heads/p280381-featureCounts-1 1739259196412031631/p280381-featureCounts-1 1739174032031339786/tmp_refs/heads/p280381-featureCounts-1 1739174032031339786/p280381-featureCounts-1 1739056969309805543/tmp_refs/heads/p280381-featureCounts-1 1739056969309805543/p280381-featureCounts-1 1739031334519141227/tmp_refs/heads/p280381-featureCounts-1 1739031334519141227/p280381-featureCounts-1 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1727374536198179636/p280381-featureCounts-1 1727370158798113625/tmp_refs/heads/p280381-featureCounts-1 1727370158798113625/p280381-featureCounts-1 1727175644019938724/tmp_refs/heads/p280381-featureCounts-1 1727175644019938724/p280381-featureCounts-1 1726809703167700704/tmp_refs/heads/p280381-featureCounts-1 1726809703167700704/p280381-featureCounts-1 1726790977028873160/tmp_refs/heads/p280381-featureCounts-1 1726790977028873160/p280381-featureCounts-1 1725608452453429807/tmp_refs/heads/p280381-featureCounts-1 1725608452453429807/p280381-featureCounts-1 1725590531341194893/tmp_refs/heads/p280381-featureCounts-1 1725590531341194893/p280381-featureCounts-1 1723659217351979803/tmp_refs/heads/p280381-featureCounts-1 1723659217351979803/p280381-featureCounts-1 1723214563622943980/tmp_refs/heads/p280381-featureCounts-1 1723214563622943980/p280381-featureCounts-1 1722541877465010848/tmp_refs/heads/p280381-featureCounts-1 1722541877465010848/p280381-featureCounts-1 1720921192765419283/tmp_refs/heads/p280381-featureCounts-1 1720921192765419283/p280381-featureCounts-1 1719504011551343008/tmp_refs/heads/p280381-featureCounts-1 1719504011551343008/p280381-featureCounts-1 1717843993116610371/tmp_refs/heads/p280381-featureCounts-1 1717843993116610371/p280381-featureCounts-1 1717372367594558298/tmp_refs/heads/p280381-featureCounts-1 1717372367594558298/p280381-featureCounts-1 1717372359521408222/tmp_refs/heads/p280381-featureCounts-1 1717372359521408222/p280381-featureCounts-1 1716554888116639232/tmp_refs/heads/p280381-featureCounts-1 1716554888116639232/p280381-featureCounts-1 1711772603497484764/tmp_refs/heads/p280381-featureCounts-1 1711772603497484764/p280381-featureCounts-1 1705901069090943222/tmp_refs/heads/p280381-featureCounts-1 1705901069090943222/p280381-featureCounts-1 p280381-featureCounts-1 A.K. Saikumar Jayalatha 2021-02-12 15:54:26 +0100
• 1037d154e3 Small snippet that generates a genome index and aligns the RNAseq reads. 1739617982070452600/tmp_refs/heads/step3/star-alignment-snippet 1739617982070452600/step3/star-alignment-snippet 1739544498642452964/tmp_refs/heads/step3/star-alignment-snippet 1739544498642452964/step3/star-alignment-snippet 1739018379607846110/tmp_refs/heads/step3/star-alignment-snippet 1739018379607846110/step3/star-alignment-snippet 1738808147272312330/tmp_refs/heads/step3/star-alignment-snippet 1738808147272312330/step3/star-alignment-snippet 1738677025579241206/tmp_refs/heads/step3/star-alignment-snippet 1738677025579241206/step3/star-alignment-snippet 1738100077422143409/tmp_refs/heads/step3/star-alignment-snippet 1738100077422143409/step3/star-alignment-snippet 1736884474674729297/tmp_refs/heads/step3/star-alignment-snippet 1736884474674729297/step3/star-alignment-snippet 1736869583883684330/tmp_refs/heads/step3/star-alignment-snippet 1736869583883684330/step3/star-alignment-snippet 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1732742270794408867/tmp_refs/heads/step3/star-alignment-snippet 1732742270794408867/step3/star-alignment-snippet 1732726252147928861/tmp_refs/heads/step3/star-alignment-snippet 1732726252147928861/step3/star-alignment-snippet 1732626932907289319/tmp_refs/heads/step3/star-alignment-snippet 1732626932907289319/step3/star-alignment-snippet 1727640200620013268/tmp_refs/heads/step3/star-alignment-snippet 1727640200620013268/step3/star-alignment-snippet 1727350540102218197/tmp_refs/heads/step3/star-alignment-snippet 1727350540102218197/step3/star-alignment-snippet 1726906495184632345/tmp_refs/heads/step3/star-alignment-snippet 1726906495184632345/step3/star-alignment-snippet 1726848903758721178/tmp_refs/heads/step3/star-alignment-snippet 1726848903758721178/step3/star-alignment-snippet 1726228084253368317/tmp_refs/heads/step3/star-alignment-snippet 1726228084253368317/step3/star-alignment-snippet 1723872766261883237/tmp_refs/heads/step3/star-alignment-snippet 1723872766261883237/step3/star-alignment-snippet 1723718086292986425/tmp_refs/heads/step3/star-alignment-snippet 1723718086292986425/step3/star-alignment-snippet 1723709087297555857/tmp_refs/heads/step3/star-alignment-snippet 1723709087297555857/step3/star-alignment-snippet 1723691168040247541/tmp_refs/heads/step3/star-alignment-snippet 1723691168040247541/step3/star-alignment-snippet 1722687731330751385/tmp_refs/heads/step3/star-alignment-snippet 1722687731330751385/step3/star-alignment-snippet 1722657100665975874/tmp_refs/heads/step3/star-alignment-snippet 1722657100665975874/step3/star-alignment-snippet 1720715643819160669/tmp_refs/heads/step3/star-alignment-snippet 1720715643819160669/step3/star-alignment-snippet 1717854819277334119/tmp_refs/heads/step3/star-alignment-snippet 1717854819277334119/step3/star-alignment-snippet 1717369704380300369/tmp_refs/heads/step3/star-alignment-snippet 1717369704380300369/step3/star-alignment-snippet 1717369697520381458/tmp_refs/heads/step3/star-alignment-snippet 1717369697520381458/step3/star-alignment-snippet 1716581361394640823/tmp_refs/heads/step3/star-alignment-snippet 1716581361394640823/step3/star-alignment-snippet 1709243577600139218/tmp_refs/heads/step3/star-alignment-snippet 1709243577600139218/step3/star-alignment-snippet 1694498508496227736/tmp_refs/heads/step3/star-alignment-snippet 1694498508496227736/step3/star-alignment-snippet Hylke C. Donker 2021-02-09 17:31:42 +0100
• a7651f6a21 UMI deduplication script from Victor TatiKarp 2021-02-12 13:52:56 +0100
• d71460a7dd Tailored storage locations to calculon. 1740209982862908595/tmp_refs/heads/step3/star-alignment-snippet 1740209982862908595/step3/star-alignment-snippet 1740198064826261770/tmp_refs/heads/step3/star-alignment-snippet 1740198064826261770/step3/star-alignment-snippet 1740170954871814489/tmp_refs/heads/step3/star-alignment-snippet 1740170954871814489/step3/star-alignment-snippet 1740104136014249202/tmp_refs/heads/step3/star-alignment-snippet 1740104136014249202/step3/star-alignment-snippet 1739858415401677944/tmp_refs/heads/step3/star-alignment-snippet 1739858415401677944/step3/star-alignment-snippet 1739856092132061055/tmp_refs/heads/step3/star-alignment-snippet 1739856092132061055/step3/star-alignment-snippet 1739733380011952245/tmp_refs/heads/step3/star-alignment-snippet 1739733380011952245/step3/star-alignment-snippet 1739634642209814647/tmp_refs/heads/step3/star-alignment-snippet 1739634642209814647/step3/star-alignment-snippet 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1717369736312494710/step3/star-alignment-snippet 1717369732339091591/tmp_refs/heads/step3/star-alignment-snippet 1717369732339091591/step3/star-alignment-snippet 1717258811739462223/tmp_refs/heads/step3/star-alignment-snippet 1717258811739462223/step3/star-alignment-snippet 1717038550722447838/tmp_refs/heads/step3/star-alignment-snippet 1717038550722447838/step3/star-alignment-snippet 1716970767759219680/tmp_refs/heads/step3/star-alignment-snippet 1716970767759219680/step3/star-alignment-snippet 1716804542058728463/tmp_refs/heads/step3/star-alignment-snippet 1716804542058728463/step3/star-alignment-snippet Hylke C. Donker 2021-02-11 10:47:21 +0100
• 648cd09a0e fastqc: simple comment. trimming: reverted back. overall qc: simplified the scripts and made sure to add instructions. Jos van Nijnatten 2021-02-10 13:42:51 +0100
• ef4a25f54b Small snippet that generates a genome index and aligns the RNAseq reads. Hylke C. Donker 2021-02-09 17:31:42 +0100
• 135f231c86 Remove whitespace, MacOS specific files. Jos van Nijnatten 2021-02-09 15:39:35 +0100
• 58bd93171c Test change Jos van Nijnatten 2021-02-09 15:15:59 +0100
• 3d7c9e3b1c FastQC, Trimming, Overall QC (initial) Jos van Nijnatten 2021-02-09 12:52:44 +0100
• 7ecbc2aee9 Template structure. Hylke C. Donker 2021-02-09 11:20:27 +0100
• 0dcd6ac858 Merge branch 'feature/drone-pipeline' Hylke Cornelis Donker 2019-12-12 18:00:15 +0100
• d28fafef27 Another try of drone Hylke Cornelis Donker 2019-12-12 16:46:39 +0100
• 37bde351e1 Added Drone with R linter. Hylke Cornelis Donker 2019-12-12 16:40:57 +0100
• ae75ad9f9d Merge branch 'master' of https://git.web.rug.nl/GRIAC/system_genetics Hylke Cornelis Donker 2019-12-12 16:19:57 +0100
• 828476002a This is a test Corneel Vermeulen 2019-12-12 15:24:40 +0100
• 02d446ad5a first commit Corneel Vermeulen 2019-12-12 11:34:28 +0100
• 1dcf333571 first commit Hylke Cornelis Donker 2019-12-11 11:41:34 +0100