question about stringtie arguments

Question

[sophialovechan]

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

[sophialovechan]

I meant how I will be able to identify the value for each argument. Thanks.

Answer 1

[Devon Ryan]

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.

[sophialovechan]

Thanks for your response. I was trying to optimize everything before I run the program. But your answer makes sense. Thank you.