Hello all, hope you guys are doing well,
I have transcriptome data of Nicotiana tabacum and its genome file is available on NCBI, so I have done their alignment with reference genome with the help of STAR software and got the BAM file. so now I'm doing their assembly using the Trinity genome-guided method and was a parameter..
--genome_guided_max_intron 10000
can you please help me to understand this parameter, that how to decide the intron number?.as mentioned above 10000..
thank you
https://www.biostars.org/p/208687/
This value would depend on your data and I think you need to play a bit with the value to get best result out of your assembly. Or you can find similar studies it they mention anything related to this. But finally you have to decide it yourself and check the above link.
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