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Old 02-18-2016, 03:34 PM   #5
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Join Date: Mar 2010
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Originally Posted by mpertea View Post
It is very likely that most of the transcripts that make up the difference are intronic or intergenic single exon transcripts. Especially with such a large number of samples, there are many small fragments expressed all over the place. We are more aggressive in filtering these out in StringTie version 1.2.2 (just released today), so please give it a try.

The other ways to filter more of the transcripts are with the -f parameter just as mentioned before, or with the -F or -T parameters that filter out transcripts of very low abundance in the samples. We like filtering with -F and -T more than with the -f option, because -f filters transcripts that have a relative low abundance compared to the most abundant transcript in the bundle, even if sometimes the transcripts that are filtered out are highly expressed.
This is very helpful, thanks. One question I have would be about the merging that gffcompare does vs. the "stringtie --merge" method. It seems like "stringtie --merge" is the more appropriate method for joining libraries from different tissues, followed by an assessment with gffcompare. Is this correct? The docs say that gffcompare also does merging but it is not clear to how this relates to what "stringtie --merge" is doing.
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