GRIAC/system_genetics
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35f356dd3336f2bd8614136498982fc966114189
Commit Graph
22 Commits
Author SHA1 Message Date
Hylke C. Donker 35f356dd33 Use BAM files for htseq-count. 2021-03-17 17:06:02 +01:00
Hylke C. Donker 4b449ded08 Bug fix in trimmomatic paired-end flag. 2021-03-10 13:45:06 +01:00
Hylke C. Donker 1c42a61e48 Updated htseq-count with extra comments. 2021-02-25 16:59:57 +01:00
Hylke C. Donker e852072235 Added htseq-count snippet + updated STAR snippet indicating prebuilt genome index. 2021-02-25 12:40:17 +01:00
TatiKarp d4016b44b6 Added comments to umi deduplication 2021-02-23 15:18:35 +01:00
Hylke C. Donker f93596dd87 Made snippet input- and output files more harmonised. 2021-02-23 09:16:39 +01:00
M. Berg a2bc313515 Simple snippet on running MultiQC to collate FastQC results 2021-02-22 14:52:54 +01:00
T. Karp 981a983dd5 Merge pull request 'UMI deduplication script from Victor' (#3) from s3970582/system_genetics:master into master 
Reviewed-on: #3
 2021-02-15 17:44:30 +01:00
TatiKarp c05d3f7868 Added description and some comments for UMi deduplication 2021-02-15 17:18:48 +01:00
J.v.N. 65d7193848 Merge branch 'master' into step3/star-alignment-snippet 2021-02-15 17:08:31 +01:00
Jos van Nijnatten 6cf40804c4 adapter comments 2021-02-15 17:03:34 +01:00
Jos van Nijnatten 51abdcdb26 Trimmomatic update (simplified) 2021-02-15 16:48:39 +01:00
J.v.N. 4c52527340 Merge branch 'master' into master 2021-02-15 16:18:28 +01:00
Jos van Nijnatten 170a001729 Count reads in X and Y chromosome. 2021-02-15 12:54:31 +01:00
C. Qi 4b61c099f6 Update 'rnaseq/step2_trim/snippet.sh' 2021-02-13 19:13:13 +01:00
Hylke C. Donker 1037d154e3 Small snippet that generates a genome index and aligns the RNAseq reads. 2021-02-12 14:46:05 +01:00
TatiKarp a7651f6a21 UMI deduplication script from Victor 2021-02-12 13:52:56 +01:00
Jos van Nijnatten 648cd09a0e fastqc: simple comment. trimming: reverted back. overall qc: simplified the scripts and made sure to add instructions. 2021-02-10 13:42:51 +01:00
Jos van Nijnatten 135f231c86 Remove whitespace, MacOS specific files. 2021-02-09 15:39:35 +01:00
Jos van Nijnatten 58bd93171c Test change 2021-02-09 15:15:59 +01:00
Jos van Nijnatten 3d7c9e3b1c FastQC, Trimming, Overall QC (initial) 2021-02-09 12:52:44 +01:00
Hylke C. Donker 7ecbc2aee9 Template structure. 2021-02-09 11:20:27 +01:00