Question: Stringtie "GffNameList Error: invalid index (-1)"
gravatar for rporterfield
10 weeks ago by
rporterfield0 wrote:

Hello, I am doing some transcriptome assembly using Stringtie as well as other assemblers. I am running the assemblies with trimmed and filtered bam files and a reference genome. The other assemblers I am using are working fine with the SRA data I provide them. For some reason, Stringtie works about half of the time, and the other half returns this error "GffNameList Error: invalid index (-1) " and nothing else. I have looked at the documentation for the code and cannot make much sense of it, and there are no posts about this problem yet. I do not understand why about half of my data is running properly and the other half isn't using the same reference file.

Any help is appreciated,


ADD COMMENTlink modified 10 weeks ago by Jennifer Hillman Jackson23k • written 10 weeks ago by rporterfield0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:


I haven't seen this particular error either. But can recommend some items to check. See this prior post for how to verify the inputs and adjust mapper settings as needed. If using HISAT, the output can be specific for Stringtie or Cufflinks, but not both in the same output, due to the different expected input format from the downstream tools.

If you cannot determine the problem, a bug report can be sent in. This is how:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 10 weeks ago by Jennifer Hillman Jackson23k

Yes, the pipeline we are using has HISAT specifications for cufflinks and stringtie. This pipeline has worked many other times but has trouble with select SRA data. I am just trying to find a fix for it so we do not have to throw away any data.


ADD REPLYlink written 7 weeks ago by rporterfield0
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