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Old 04-16-2013, 05:43 AM   #4
severin
Genome Informatics Facility
 
Location: Iowa @isugif

Join Date: Sep 2009
Posts: 105
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Quote:
Originally Posted by Tka View Post
Thank you for the reply and I will try to be a little more specific.

The experiment design included 3 biological replicates for different temperature points. It's biological soil samples but the coverage is unknown. Only thing I know is that the number of reads (Illumina) for each sample is the same. I have a reference that is either included in the sample or has multiple very closely related strains in it.

By the way: sorry for asking real basic questions. Just started with transcriptomics and didn't think about de novo assembly, yet. Could you hint me to some tools that map de novo assembled transcripts to a reference genome?

Thanke you very much,

Tka

In diagram form.

Take all raw read files -> Trinity assembly program -> assembled scaffolds
take each raw reads -> align using GSNAP alignment program to assembled scaffolds -> SAM output
take assembled scaffolds -> metageneMark -> gene models gff file
use aligned file, gff file and htseq-count --stranded=no to generate count information on a per gene basis for your denovo assembled transcripts
blast gene models against NR to determine function of genes.

Good luck!
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