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readme update
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jethror1 committed Jul 7, 2021
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Expand Up @@ -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.<br>
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