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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 +01:00
• 4b449ded08 Bug fix in trimmomatic paired-end flag. Hylke C. Donker 2021-03-10 13:45:06 +01:00
• 1c42a61e48 Updated htseq-count with extra comments. Hylke C. Donker 2021-02-25 16:59:57 +01:00
• e852072235 Added htseq-count snippet + updated STAR snippet indicating prebuilt genome index. Hylke C. Donker 2021-02-25 12:40:17 +01:00
• 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 +01:00
• d4016b44b6 Added comments to umi deduplication 1740291789975933683/tmp_refs/heads/master 1740291789975933683/master 1740291003645797583/tmp_refs/heads/master 1740291003645797583/master 1740290781630099559/tmp_refs/heads/master 1740290781630099559/master 1740268871901661533/tmp_refs/heads/master 1740268871901661533/master 1740267065753837732/tmp_refs/heads/master 1740267065753837732/master 1740266213379742228/tmp_refs/heads/master 1740266213379742228/master 1740265215068046678/tmp_refs/heads/master 1740265215068046678/master 1740264994659730744/tmp_refs/heads/master 1740264994659730744/master 1740264912587040798/tmp_refs/heads/master 1740264912587040798/master 1740264408517287999/tmp_refs/heads/master 1740264408517287999/master 1740264221698287757/tmp_refs/heads/master 1740264221698287757/master 1740263917295302798/tmp_refs/heads/master 1740263917295302798/master 1740246756943752520/tmp_refs/heads/master 1740246756943752520/master 1740246291721372883/tmp_refs/heads/master 1740246291721372883/master 1740246236120474083/tmp_refs/heads/master 1740246236120474083/master 1740246163441429576/tmp_refs/heads/master 1740246163441429576/master 1740244923265773616/tmp_refs/heads/master 1740244923265773616/master 1740241964990096331/tmp_refs/heads/master 1740241964990096331/master 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 +01:00
• 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 +01:00
• 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 +01:00
• f93596dd87 Made snippet input- and output files more harmonised. Hylke C. Donker 2021-02-22 13:18:18 +01:00
• a2bc313515 Simple snippet on running MultiQC to collate FastQC results M. Berg 2021-02-22 14:52:54 +01:00
• 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 +01:00
• c05d3f7868 Added description and some comments for UMi deduplication TatiKarp 2021-02-15 17:18:48 +01:00
• 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 +01:00
• 65d7193848 Merge branch 'master' into step3/star-alignment-snippet step3/star-alignment-snippet J.v.N. 2021-02-15 17:08:31 +01:00
• cba83716c8 Merge pull request 'Trimmomatic update (simplified)' (#5) from P300299/system_genetics:master into master J.v.N. 2021-02-15 17:06:31 +01:00
• 6cf40804c4 adapter comments Jos van Nijnatten 2021-02-15 17:03:34 +01:00
• 51abdcdb26 Trimmomatic update (simplified) Jos van Nijnatten 2021-02-15 16:48:39 +01:00
• 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 +01:00
• 4c52527340 Merge branch 'master' into master J.v.N. 2021-02-15 16:18:28 +01:00
• 170a001729 Count reads in X and Y chromosome. Jos van Nijnatten 2021-02-15 12:54:31 +01:00
• 4b61c099f6 Update 'rnaseq/step2_trim/snippet.sh' C. Qi 2021-02-13 19:13:13 +01:00
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Saikumar Jayalatha 2021-02-12 15:54:26 +01:00
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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 +01:00
• a7651f6a21 UMI deduplication script from Victor TatiKarp 2021-02-12 13:52:56 +01:00
• 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 +01:00
• 135f231c86 Remove whitespace, MacOS specific files. Jos van Nijnatten 2021-02-09 15:39:35 +01:00
• 58bd93171c Test change Jos van Nijnatten 2021-02-09 15:15:59 +01:00
• 3d7c9e3b1c FastQC, Trimming, Overall QC (initial) Jos van Nijnatten 2021-02-09 12:52:44 +01:00
• 7ecbc2aee9 Template structure. Hylke C. Donker 2021-02-09 11:20:27 +01:00
• 0dcd6ac858 Merge branch 'feature/drone-pipeline' Hylke Cornelis Donker 2019-12-12 18:00:15 +01:00
• d28fafef27 Another try of drone Hylke Cornelis Donker 2019-12-12 16:46:39 +01:00
• 37bde351e1 Added Drone with R linter. Hylke Cornelis Donker 2019-12-12 16:40:57 +01:00
• ae75ad9f9d Merge branch 'master' of https://git.web.rug.nl/GRIAC/system_genetics Hylke Cornelis Donker 2019-12-12 16:19:57 +01:00
• 828476002a This is a test Corneel Vermeulen 2019-12-12 15:24:40 +01:00
• 02d446ad5a first commit Corneel Vermeulen 2019-12-12 11:34:28 +01:00
• 1dcf333571 first commit Hylke Cornelis Donker 2019-12-11 11:41:34 +01:00