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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--
Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
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