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Question: Salmon: Error while indexing Human transcriptome file
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gravatar for syrez
18 months ago by
syrez • 0
Chicago
syrez • 0 wrote:

Hi there!

I downloaded what I hope to be a human transcriptome data file from biomart. I select for gene types in Gene, cDNA Sequences in Attributes and in header info, I pick Gene Stable ID and Transcript ID. The downloaded file is in txt format.

When I initiate salmon to index the file salmon index -t ~/path/mart_export.txt -i hg38_index

I get the following :

error Building suffix array . . . FAILURE: return code from libdivsufsort() was -1

Could anyone please help me with this?

Thanks!
salmon • 660 views
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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 18 months ago by syrez • 0
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gravatar for Jennifer Hillman Jackson
18 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I would check two items when importing sequence data this way:

  1. The load from was complete. Transcriptomes can be quite large and it is usually better to download these in fasta format from the source, then upload to Galaxy with FTP.

  2. This tool accepts fasta format. The tool Tabular-to-FASTA converts a tabular file to FASTA format. Also be sure to follow the guidelines for Custom genome formatting here (the same format rules apply for your use case): https://galaxyproject.org/learn/custom-genomes/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
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