Hi, I am learning the StringTie to assemble my sequencing data now. But I am not sure about serveral arguments and also didn't find any references. So I am wondering if anyone can give me a hand on this.
-m <int> Sets the minimum length allowed for the predicted transcripts. Default: 200
-a <int> Junctions that don't have spliced reads that align across them with at least this amount of bases on both sides are filtered out. Default: 10
-j <float> There should be at least this many spliced reads that align across a junction (i.e. junction coverage). This number can be fractional, since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the junction coverage. Default: 1
-c <float> Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2.5
-g <int> Minimum locus gap separation value. Reads that are mapped closer than this distance are merged together in the same processing bundle. Default: 50 (bp)
Thank you so much