variable read length clarification

[Joe Ellis]

Hi,

my group was discussing the --variable-read-length option and I was wondering if there is a threshold for rMATS for what is acceptable deviation from the supplied --read-length flag? Moreover, if I were to use --read-length 75 what deviations in length would rMATS accept? Would a read of 200 be used? 100? 50? 

Thanks

-Joe

[kutsc...@gmail.com]

With --variable-read-length, reads of any length will be used. Here is a post with more details: https://github.com/Xinglab/rmats-turbo/issues/83

There is no threshold for acceptable deviation in rMATS. Here is the inclusion level calculation: https://github.com/Xinglab/rmats-turbo/blob/v4.1.2/rMATS_P/inclusion_level.py#L24

The inclusion level calculation uses the effective length shown in the diagram at: https://github.com/Xinglab/rmats-turbo/tree/v4.1.2#output

Small changes to the read length value should not change the calculation much. You can run rMATS with different values to see how the results change

Eric