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Old 03-03-2016, 11:44 AM   #5
moldach
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Location: Vienna

Join Date: Jan 2016
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Quote:
Originally Posted by colindaven View Post
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#1 Remap reads to closely related genome. Satisfied with mapping rate ?
I had tried mapping at one point some-time-ago to the closely related un-annotated genome. Unfortunately, I used Bowtie2. I now know better; you need to use a splice-junction aware aligner.

Quote:
Originally Posted by colindaven View Post
Suggestions
#2 Use gmap (easy) or Maker to map your de novo assembled transcripts to the related genome. Again, satisfied ? View both sets in a genome browser.
So GMAP maps and aligns with this command:

>gmap -d <genome> -A <cdna_file>

And it would output SAM files.

What I don't understand is how (or if) GMAP annotates this genome?
The documentation for maker on the other hand clearly states it annotates but I can't find anything in the GMAP documentation.

Will gmap and Maker output an annotation file including chromosomal coordinates of features (GTF)? It says that this is a required file to use featureCounts
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