Issue with gffread during converting gtf file to fasta
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4.3 years ago
seta ★ 1.5k

Hi all,

I used cufflinks package for genome-guided transcriptome assembly, followed by using gffread for converting the produced gtf file to fasta file, but some warnings (like below) appeared during this conversion,

Warning: couldn't find fasta record for 'HSCHR6_MHC_SSTO'!
Warning: getSpliced(NULL,.. ) called!

Could you please let me know what's the warning and if it's important?

Thanks

gtf file fasta gffread • 1.5k views
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Entering edit mode

Seems like genome fasta and genome annotation are from different sources or versions.

But it would be helpful if you provide more details to your question.

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