[maker-devel] advanced repeat masking library constructions & rna-seq assembly choices

[Salim Bougouffa]

Hi,

I am attempting to annotate a plant genome. I have a couple of questions:

*1) RNA-seq assembly*
a) I assembled my RNA-seq data using Trinity and StringTie. The two produce
drastically different numbers. When I compare the two assemblies for each
sample using TransRate, StringTie produces a higher score. for most of the
assemblies. I see in all of the threads that you recommend Trinity but
doesn't trinity produce way too many transcripts (even after chucking out
the "bad" ones using transrate).
b) During hint creation in MAKER, does it take into account that different
transcripts have different read coverage (expression levels). I guess my
question is should I filter transcripts that have a small read coverage.

*2) Repeat Masking *
I am following the advanced repeat library construction tutorial (
http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced).
The initial steps find 15 sequences for the LTR and 159 for MITE. But, when
I get to the perl DIR_CRL/CRL_Step4.pl step, both output files
(Inner_Seq_For_BLAST.fasta, lLTRs_Seq_For_BLAST.fasta) are empty.

a) are these numbers normal because I was expecting a lot more than 16 for
the LTR?
b) I don't get any errors when I run CRL_Step4.pl yet no output. What's
going on?!

Many thanks,
/SB
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