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Old 02-07-2017, 07:46 PM   #7
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Originally Posted by mcsimenc View Post
Can anyone suggest an interpretation of the following results using stringtie --merge: ?

Three stringtie assemblies with 29747, 30865, and 29863 transcripts are merged using stringtie --merge and the resulting gtf has only 25130 transcripts.

Am I losing information? I do not know the internal workings of stringtie --merge but I intuitively expect to have no fewer transcripts than the input assembly with the fewest transcripts.

Hello Matt,

According to my understanding, the number of merged transcripts presented depends on the relative expression of the input transcript files. As the literature stares, " generate a non-redundant set of transcripts observed in all the RNA-Seq samples assembled previously to generate a a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples." which means, the merge option will only produce transcripts with robust expression (or whatever expression cutoff one selects). Are you using a reference transcriptome file in assembly? you can also use gff compare to check the accuracy of your files.

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