Question: Salmon: Error while indexing Human transcriptome file
gravatar for syrez
8 months ago by
syrez0 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?


salmon • 262 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson23k • written 8 months ago by syrez0
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson23k wrote:


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):

Thanks! Jen, Galaxy team

ADD COMMENTlink written 8 months ago by Jennifer Hillman Jackson23k
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