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Galaxy DNA-seq, RNA-seq alignment

I have personal Galaxy instance running on centOS 7. I am having issue with Bowtie2 and HISAT2. It's the same error on both.

I think it is an issue with Genome index.

Steps for getting Genome into local Galaxy instance.

  1. Fetch Genome into local galaxy using "Get data USCS Main table".
  2. Build index using Bowtie2 index builder (Galaxy Version 2.3.5.1+galaxy1).
  3. Upload FASTQ files into Galaxy.
  4. FastQC Read Quality reports (Galaxy Version 0.72+galaxy1).
  5. FASTQ Masker by quality score (Galaxy Version 1.1.5)
  6. Bowtie2 - map reads against reference genome (Galaxy Version 2.3.4.3+galaxy0).

Input: FASTQ Masker file from Step 5, Use a built-in index and select reference genome built in Step 2.

This is where I get the following error and this is same with HISAT2.

[E::idx_find_and_load] Could not retrieve index file for '/home/webuser/galaxy/database/objects/6/7/d/dataset_67dde163-6ec6-4f51-afa6-f8aa2aee66b0.dat'

Any input is greatly appreciated.

Thank you.

alignment bowtie
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updated by ATpoint ATpoint • written by sunila_mahavadi • sunila_mahavadi

Hello, you might want to post this over at the Galaxy support forum https://help.galaxyproject.org/. Please always add relevant code to your questions, thank you!

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written by ATpoint ATpoint

Hello sunila_mahavadi!

We believe that this post does not fit the main topic of this site.

Like ATPoint said, please ask this on Galaxy forum.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by Ram Ram

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