Question: stringtie error in refernce genome file
gravatar for shafnaasmy.v.s
19 months ago by
shafnaasmy.v.s10 wrote:


i m working on human datasets i tired running stringtie with the bam file from hisat....i get error saying

Fatal error: Exit code 1 () Error: invalid genomic sequence data (NW_003315959.1)!

i tried it using the gff,gff3 and gtf files of the refernce genome of homosaipens

plz help

thanks in advance

rna-seq stringtie • 940 views
ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson25k • written 19 months ago by shafnaasmy.v.s10
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:


There is most likely a chromosome identifier mismatch problem between the reference annotation and the reference genome. These must be exact for all inputs, for most tools, including these used for RNA-seq analysis.

Please see this help for how to check/fix the problem:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k
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