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Old 01-03-2012, 09:46 AM   #8
Genome Informatics Facility
Location: Iowa @isugif

Join Date: Sep 2009
Posts: 105

I would start by looking at the reference that Jon Keats provided as it will likely provide information on how other people have solved your particular problem in the past on Humans and tumor cells. It is always good to be able to reference a paper and say we did it the same as these people.

Originally Posted by angerusso View Post
Here are the answers to your questions. Thanks so much again. I will wait for the replies.

1. Do you have a particular organism that you are working with?
- Human

2. Do you have the fasta file of the genes that you want the lengths of?
- No

3. Do you want the length of the cDNA or the genes with introns?
- The data is generated using Illumina (Exome sequencing)
- So I understand I need the length of all exons in a gene (how would I get this info for a set of 1000 genes?). Am I right?

4. Do you care about splice variants or will the longest splice variant?
- well, I don't know the answer. Should I consider the entire exon length as the length of the longest transcript?
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