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Add input file download instructions to SpliceAI header #774

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@ainefairbrother ainefairbrother commented Feb 10, 2025

JIRA ticket: ENSVAR-6685

Added the following to the header section of SpliceAI.pm to explain in more detail to users how to download the files as it's not super obvious:

The files with the annotations for all possible substitutions (snv), 1 base insertions
and 1-4 base deletions (indel) within genes are available here https://basespace.illumina.com/s/otSPW8hnhaZR,
and can be accessed as follows:

  1. Log-in to your Illumina account or sign-up if you don't have one.
  2. Once you're in, a "Share Project" pop-up will appear - click "accept".
  3. A smaller pop-up in the bottom right will read "Share Accepted". Click "Predicting splicing from primary sequence".
  4. You will get a list of files. Select "genome_scores_v1.3".
  5. You will get an info/landing page. Under "Analysis: genome_scores_v1.3", select "FILES".
  6. Click the file icon next to "genome_scores_v1.3" and you will get a list of available files.
  7. Click filenames to download the relevant files - note that raw/masked, hg19/hg38 and snv/indel files are available.

Also fixed reference to hg37 > hg19.

@dglemos dglemos self-requested a review February 10, 2025 14:44
@dglemos dglemos self-assigned this Feb 10, 2025
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