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

[Israel Barrantes]

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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