Question: Reference genome on Bowtie2
gravatar for gomez.andreia
2.1 years ago by
gomez.andreia0 wrote:

Dear Galaxy support team,

My name is Andreia and I am writing you because I am having trouble mapping ChIP-seq samples to human genome reference using local Galaxy. I have installed Bowtie2 although it does not contain the genome reference, and as an alternative I tried to upload via FTP, unsuccessfully.

Could you please tell me whether I need to install a genome reference package or how may I overcome the upload of a file bigger than 2Gb?

My best regards,


ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by gomez.andreia0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I would suggest using Data Managers since you are running a local. Custom genomes take up more resources, every job.

The source Fasta can be loaded from a history if it is not on a public server and used with DMs (from the Tool Shed installed then used as Admin). There are two fasta installers - use the one that includes a "dbkey" if creating your own (not already in the genome list - Upload or Edit Attributes).

To load large data (genomes, other experimental data), enable FTP on the instance or load larger files directly into a Library from the file system (then move data lib > history for use). Or do both as needed!

Best, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k

Bit more help if go the DM route. Install/run indexes in this order:

  1. Fetch fasta (allow to complete). If pulling from UCSC, only retrieve 2 at a time or the jobs will fail (UCSC has a concurrent-access limit). Should that happen by mistake, just rerun.
  2. Ensure that 1 is intact, then Samtools indexes (allow to complete)
  3. Ensure that 2 is intact, Picard indexes (allow to complete)
  4. Ensure that 1,2,3 are intact, then launch twoBit indexes (can execute 5 - below - while this is running) -- ALWAYS do the first 4, every genome, and do it first
  5. Install any other indexes that you want to. If you run into memory/resource failures, run one at a time.

ps: The Bowtie2 DM as an option to create Tophat indexes at the same time. This is almost always a good idea. It is difficult and can create conflicts/duplicates in your instance if you run this DM again just to create Tophat indexes later.

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k
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