error cdna_alignment_orf_to_genome_orf.pl

[Alicia Talavera]

Hello TransDecoder group,  

After I used hisat, stringtie, gffread to generate  the transcript file and to convert gtf to gff3, I've run TransDecoder.LongOrfs -t transcripts.fasta  and TransDecoder.Predict -t transcripts.fasta. However, when I tried to run cdna_aligment_orf_to_genome_orf.pl, I got the following error: 

Error, cannot parse ID from info [ID=MSTRG.2.1;geneID=MSTRG.2

] of line A101Chr1 StringTie transcript 173711 183525 1000 - . ID=MSTRG.2.1;geneID=MSTRG.2

This information is the same that the first line of my sample.gff3 file. Have seen anything similar before? Could you please help me? Any advice would be welcomed. 

Thank you, 

Best, 

[Brian Haas]

Hi,

If you could send me your inputs and full command line being run for that step, I'll aim to debug it directly.

bh...@broadinstitute.org

best,

~brian

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Brian Haas]

Hi Alicia,

Thanks for sending your inputs.

Your stringtie gff3 file looks different from what was expected.

An example for stringtie is provided in transdecoder under:

TransDecoder/sample_data/stringtie_example

including runMe.sh for demonstration purposes.

This starts with a stringtie gtf formatted file, which we convert to alignment-gff3 format.

hope this helps,

~brian

[Alicia Talavera]

Thank you for your help Brian,

Best, 

Alicia

--

Alicia Talavera Júdez, Ph.D.Student

Department of Subtropical and mediterranean fruit crops.

Estación Experimental IHSM La Mayora (CSIC-UMA)

29750 Algarrobo-Costa, Málaga (Spain)

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