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Someone has to run the template file TopHat???? Problems: with GTF
Someone has to run the template file TopHat???? Problems: with GTF
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Hi,
I dont have a GTF file, but I have a multifasta file with genes annotation. You know if can i use this file for mapping? how? I have converter this fasta file in GTF format? you know how?
ThanksComment
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Hi!
Wanted to bump this thread up a bit:
What happens if you have pseudogenes? Will using tophat with a reference annotation (ex. the Gencode12 Comprehensive, which does not include pseudogenes), bias you against proper mapping of reads to these regions?Comment
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I am also wondering about this and would be interested in hearing an answer.Originally posted by dvanic View PostComment
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I would also be interested in a clear answer to this question.
My worry is that by supplying tophat with an annotation file if it is then biased toward aligning to genes in the annotation instead of potentially novel genes.Comment
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