How to ingest a bam file for a pileup track

[bistace]

Hello,

the higlass.io website shows a really nice visualization for a pileup track but I can't find an ingest command that would allow me to display it via the interface.

Could you please help me?

[pkerpedjiev]

Hi there! It's not officially support in higlass-manage yet but you can still you use it like this:

1. First put your BAM and BAI files in some directory. In my case I put them in /Users/pete/tmp/media
2. Start higlass using that as the media directory: higlass-manage start --no-public-data -m /Users/pete/tmp/media
3. Ingest those files by:
   a) Starting the higlass shell: higlass-manage shell
   b) Running the ingest command:

python higlass-server/manage.py ingest_tileset \
  --filename SRR1770413.sorted.short.bam \
  --indexfile SRR1770413.sorted.short.bam.bai \
  --filetype bam --datatype reads --no-upload

If you open your local higlass (http://localhost:8989), you should be able to add the BAM file the same way you add any track:

If all goes well you should be able to view your file:

There's some work happening that should improve this workflow shortly. I'll post an update when it's available.

[bistace]

Hi and thank you, that worked perfectly!