GFF read utility (included as a part of cufflinks)

syintel87 · 02-07-2013, 01:05 PM

From reference genome, if I want to extract sequences based on annotation file in order to create new fasta file,
does gffread utility exclude intron regions?

(reference.fasta + annotation.gtf => gffread utility => annotation + exon sequence)

Thank you in advance.

yzzhang · 05-02-2013, 11:53 AM

Hello, have you done with gffread successfully? I used tophat- cufflinks to analyze my 12 samples, and got a merged.gtf using cuffmerge. I wanted to discard those single exon transcripts and extract the coding sequence and protein sequence. My merged.gtf is 180 Mb and my genome is 280 Mb. I just ran gffread command and I got the gff file and exon sequence using -w argument, but I just got empty cds file and protein file when I used -x and -y argument.
Did you face this condition?
Any help is appreciated.
Best Regards,
yun

syintel87 · 05-02-2013, 02:59 PM

I am sorry, but it did not seem to work properly in my case, so that I wrote my own code using python in order to extract CDS from reference genome file.

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02-07-2013, 01:05 PM	#1
syintel87 Member Location: Universe Join Date: Dec 2012 Posts: 81	GFF read utility (included as a part of cufflinks) From reference genome, if I want to extract sequences based on annotation file in order to create new fasta file, does gffread utility exclude intron regions? (reference.fasta + annotation.gtf => gffread utility => annotation + exon sequence) Thank you in advance. Last edited by syintel87; 02-07-2013 at 01:07 PM.

05-02-2013, 02:59 PM	#3
syintel87 Member Location: Universe Join Date: Dec 2012 Posts: 81	I am sorry, but it did not seem to work properly in my case, so that I wrote my own code using python in order to extract CDS from reference genome file. Last edited by syintel87; 05-03-2013 at 06:44 AM.

05-02-2013, 11:53 AM	#2
yzzhang Member Location: florida Join Date: Jan 2013 Posts: 67	Hello, have you done with gffread successfully? I used tophat- cufflinks to analyze my 12 samples, and got a merged.gtf using cuffmerge. I wanted to discard those single exon transcripts and extract the coding sequence and protein sequence. My merged.gtf is 180 Mb and my genome is 280 Mb. I just ran gffread command and I got the gff file and exon sequence using -w argument, but I just got empty cds file and protein file when I used -x and -y argument. Did you face this condition? Any help is appreciated. Best Regards, yun