hello, jen

Thank you for your reply. I though it will return the GC content of each exon. I try it and find that the Galaxy will interpret features.

Thank you.

John

From: Jennifer Jackson

Sent: Wednesday, September 18, 2013 6:38 AM

To: 师云

Cc: galaxy-user@lists.bx.psu.edu

Subject: Re: [galaxy-user] How to calculate GC content of transcripts only including exons from a GTF file

Hello,

You can use the tool "Fetch Sequences -> Extract Genomic DNA" with a GTF file and a custom reference genome to get the fasta sequence. Instructions are here for Custom Genomes in general and "Tools on the Main Server" covers this tool:

http://wiki.galaxyproject.org/Support#Custom_reference_genome

The tool "EMBOSS -> geecee" can be used to perform the calculation on the resulting fasta sequences.

Best,

Jen
Galaxy team

On 9/10/13 11:14 PM, 师云 wrote:

Hi everyone,

I want to calculate GC content of transcripts in the gtf file like this:

chr1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1";
chr1 Cufflinks exon 3 10 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; exon_number "1";
chr1 Cufflinks exon 13 18 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; exon_number "2";
chr1 Cufflinks exon 20 22 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; exon_number "3";

and the genome sequence that transcript comes from is:

>chr1
GTAGCGTCTCCGACGCGGATATGACCGCACGCTGATGCTCCCAGGGATGAGAGGCGTGCG

I have to calculate GC content of the transcript after getting the sequence of the transcript.

So how can I get the sequence of the transcript. In this case, it would be AGCGTCTC + ACGCGG + TAT, meaning
the transcript sequence would be AGCGTCTCACGCGGTAT.

Is it possible in the Galaxy?
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