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Question: stringtie error in refernce genome file
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gravatar for shafnaasmy.v.s
19 months ago by
shafnaasmy.v.s • 10
shafnaasmy.v.s • 10 wrote:

hi

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
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modified 18 months ago by Jennifer Hillman Jackson ♦ 25k • written 19 months ago by shafnaasmy.v.s • 10
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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,

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: https://galaxyproject.org/support/chrom-identifiers/

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