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