Empty file generation

[kittyBS]

Hi!
Firstly thank you for the tool.
I try to use my gffcompare gtf output for my analysis. I have tried "/archive/yildize/alotaibi_lab/human_data/transdecoder/TransDecoder-TransDecoder-v5.5.0/util/gtf_to_alignment_gff3.pl /archive/yildize/alotaibi_lab/human_data/gffcompare/filtered_gffcompare.gtf > /archive/yildize/alotaibi_lab/human_data/transdecoder/transcripts.gff3" by taking "## generate alignment gff3 formatted output
../../util/gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3" as a reference from sampledata .sh but it creates empty transcripts.gff3 file. Also I tried "til/gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta " but also create a empty fasta file.
How can I overcome the problem?
Thank you in advance for your interest.

[brianjohnhaas]

Hi, You might need to use a different tool to extract your cdna sequences based on the gff formatting. There's a tool called gffread that might work: https://github.com/gpertea/gffread

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On Tue, Jan 16, 2024 at 9:36 AM kittyBS ***@***.***> wrote: Hi! Firstly thank you for the tool. I try to use my gffcompare gtf output for my analysis. I have tried "/archive/yildize/alotaibi_lab/human_data/transdecoder/TransDecoder-TransDecoder-v5.5.0/util/ gtf_to_alignment_gff3.pl /archive/yildize/alotaibi_lab/human_data/gffcompare/filtered_gffcompare.gtf > /archive/yildize/alotaibi_lab/human_data/transdecoder/transcripts.gff3" by taking "## generate alignment gff3 formatted output ../../util/gtf_to_alignment_gff3.pl transcripts.gtf > transcripts.gff3" as a reference from sampledata .sh but it creates empty transcripts.gff3 file. Also I tried "til/gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta " but also create a empty fasta file. How can I overcome the problem? Thank you in advance for your interest. — Reply to this email directly, view it on GitHub <#193>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZRKX3N6YI33WMFGA763OTYOY3XZAVCNFSM6AAAAABB4MZBJGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA4DGMZRGE4DIMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

[kittyBS]

Thank you for your quick return.