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
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sophialovechan •
As a general rule, start with the defaults for new tools. If, upon inspection, the results seem to be suboptimal, then and only then does it makes sense to adjust parameters.
Thanks for your response. I was trying to optimize everything before I run the program. But your answer makes sense. Thank you.
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I meant how I will be able to identify the value for each argument. Thanks.