From 43f70e077eb28736a20dde5edf427ae498642185 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:04:43 +0100 Subject: [PATCH 1/5] add file formatting to readme --- README.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7639ef5d..c07ef962 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,15 @@ The general workflow for generating the statistics and report is as follows:
@@ -39,7 +48,7 @@ Expected inputs: ``` -p / --panel_bed : Input panel bed file; must have ONLY the following 4 columns chromosome, start position, end position, gene/transcript --t / --transcript_file : Transcript annotation file, contains required gene and exon information. must have ONLY the following 6 columns: +-t / --transcript_file : Transcript annotation file, contains required gene and exon information. Must have ONLY the following 6 columns: chromosome, start, end, gene, transcript, exon -c / --coverage_file : Per base coverage file (output from mosdepth or similar) From 4cd2dd5d5d093400a0ed83ae4920117f76242791 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:23:29 +0100 Subject: [PATCH 2/5] add link to page for generating transcript file to readme --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index c07ef962..c28fdd26 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,7 @@ As a minimum, Athena requires 3 input files. These are a bed file for the gene p - transcript file: `chromosome start end gene transcript exon` - coverage file: `chromsome start end coverage` +n.b. the process for creating the transcript file may be found [here][transcript-file-url] ### Annotating BED file The BED file containing regions of interest is first required to be annotated with gene, exon and coverage information prior to analysis. This may be done using [BEDtools intersect][bedtools-intersect-url], with a file containing transcript to gene and exon information, and then the per base coverage data. Currently, 100% overlap is required between coordinates in the panel bed file and the transcript annotation file, therefore you must ensure any added flank regions etc. are the same.
@@ -146,3 +147,4 @@ Any bugs or suggestions for improvements please raise an issue. [mosdepth-url]: https://github.com/brentp/mosdepth [dx-url]: https://github.com/eastgenomics/eggd_athena +[transcript-file-url]: https://cuhbioinformatics.atlassian.net/wiki/spaces/P/pages/2241101840/Generating+transcripts+file+for+Athena From 8b4b7a6b2fff0b4686a625bf9feed795408f26df Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:24:50 +0100 Subject: [PATCH 3/5] tidy readme --- README.md | 7 ------- 1 file changed, 7 deletions(-) diff --git a/README.md b/README.md index c28fdd26..209d9598 100644 --- a/README.md +++ b/README.md @@ -125,13 +125,6 @@ $ python3 bin/coverage_report_single.py --gene_stats output/sample1-exon-coverag ``` -### For development - -Features to be developed: -- Generate run level statistics from multiple samples -- Generate run level report from multiple samples -- Add interactive elements to tables to increase useability (i.e sorting, filtering, searching) - Any bugs or suggestions for improvements please raise an issue. From bd84c056cb3293e2776e30d5c55a5d82a4ca1394 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:41:45 +0100 Subject: [PATCH 4/5] readme typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 209d9598..563d98d5 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ As a minimum, Athena requires 3 input files. These are a bed file for the gene p - panel bed file: `chromosome start end transcript` - transcript file: `chromosome start end gene transcript exon` -- coverage file: `chromsome start end coverage` +- coverage file: `chromosome start end coverage` n.b. the process for creating the transcript file may be found [here][transcript-file-url] From 5fa65976eced9c977301be223b4a228137af1da2 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:44:14 +0100 Subject: [PATCH 5/5] readme update --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 563d98d5..f8201a5a 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ As a minimum, Athena requires 3 input files. These are a bed file for the gene p - transcript file: `chromosome start end gene transcript exon` - coverage file: `chromosome start end coverage` -n.b. the process for creating the transcript file may be found [here][transcript-file-url] +n.b. the process for creating the transcript file may be found [here][transcript-file-url]. ### Annotating BED file The BED file containing regions of interest is first required to be annotated with gene, exon and coverage information prior to analysis. This may be done using [BEDtools intersect][bedtools-intersect-url], with a file containing transcript to gene and exon information, and then the per base coverage data. Currently, 100% overlap is required between coordinates in the panel bed file and the transcript annotation file, therefore you must ensure any added flank regions etc. are the same.