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Old 06-30-2015, 04:43 PM   #5
imsharmanitin
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Location: cambridge,UK

Join Date: Dec 2014
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Quote:
Originally Posted by GenoMax View Post
That is correct. When you are using --transcriptome-only option consider additional options (e.g. -T) that become relevant (scroll down to find the --transcriptome-only option section): https://ccb.jhu.edu/software/tophat/manual.shtml#toph.
If i understood correctly, when we use the --transcriptome-index without -T then the reads will be first mapped to the transcriptome-index and the reads which fail to match will be mapped to genome (just like using only -G option)

on the other hand if i use -T then mapping will happen only with transcriptome and report only those mappings as genomic mappings.

if i want to map to genome only then use of -G and -T should be avoided.

Also as far i have read and understood mapping to both transcriptome and genome will be an ideal approach i.e. use of -T should be avoided. Am I right?
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