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Question: transcript assembly using StringTie
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gravatar for sapna01t
20 months ago by
sapna01t • 30
sapna01t • 30 wrote:

I am trying to do assembly using stringtie, but i am getting error:

Fatal error: Exit code 1 () Warning: invalid GTF record, transcript_id not found:

My GFF file looks like this Seqname Source Feature Start End Score Strand Frame Attributes A01 GeneWise gene 3352 5985 1195.88 + . transcript_id "BjuA000594"; A01 GeneWise transcript 3352 5985 1195.88 + . transcript_id "BjuA000594";Parent "BjuA000594"; A01 GeneWise exon 3352 3675 1195.88 + 0 transcript_id "BjuA000594.cds";Parent "BjuA000594";

I have edited its attribute from gene_id to transcript _id ... Is it the right way?? Please suggest me, what should I do?
transcript assembly assembly stringtie • 966 views
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modified 20 months ago by Mo Heydarian ♦ 830 • written 20 months ago by sapna01t • 30
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gravatar for Mo Heydarian
20 months ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hello, Do you get the same error if you use the unmodified GFF file? If not, you likely need to modify the GFF file to preserve the format of the data in the "attributes" column.

Hope this helps!

Thanks for using Galaxy!

Cheers, Mo Heydarian
ADD COMMENT • link written 20 months ago by Mo Heydarian ♦ 830
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