[maker-devel] different RNA-seq experiment outputs in separate annotation passes?

[Daniel Ence]

Hi Israel,

I think that for general annotation purposes, you want to use all of those GFF files during your one make run to annotate the whole genome. If you're interested in exploring which genes are expressed in your different strains and cell stages, then you can use your annotation results and blast against the different RNA-seq experiments.

I didn't answer your questions separately, but hopefully that gives some good guidance. If I missed something, let me know.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________
From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Israel Barrantes [isradelacon at gmail.com]
Sent: Monday, March 11, 2013 12:34 PM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] different RNA-seq experiment outputs in separate annotation passes?

Dear maker-devel,

I have several RNA-seq experiment outputs that I want to use as input for MAKER annotation:
(1) Illumina 1.3, strain A, cell stage N
(2) Illumina 1.8, strain A, cell stage N
(3) Illumina 1.8, strain B, cell stage N
(4) 454, strain unknown, cell stage M
For each experiment I mapped the reads and produced GTFs with tophat/cufflinks separately (and later converted to GFF3s with the supplied script)

Q1: Does it make a difference to run a different annotation pass for each GFF3 from tophat/cufflinks?
Q2: If this is the case, altering the order of passing the cDNA GFFs (e.g., first pass, experiment 1 GFF, then exp.2 in second pass, etc) will produce more or less transcripts?
Q3: Is it better to simply merge this GFFs into a single nonredundant file (e.g. bedtools intersect) than using them separately, one for each MAKER pass?

Thank you in advance,


--
Israel Barrantes
Otto-von-Guericke-Universität
Lehrstuhl für Regulationsbiologie IBIO/FNW
Deutschland

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