Meaning of Intron Motifs

[Omar El Garwany]

Hi Alex and others

Thanks for developing STAR. Such a great tool. I just had a couple of question about the SJ.out.tab file and STAR's default behaviour with the two-pass mode.

1-So in the documentaion, column5 of the file is coded as 0 if the splice site is non-canonical and 1,2,...6 for a number of other sequences. Are the values > 0 considered canonical splice motifs? If so, is this based on a certain definition of canonical motifs? 

2-I had another question about the default STAR behaviour when I use the --twoPassMode Basic flag. What happens when I don't specify any --outSJfilter paramaters. Is the default behaviour to apply the default filters, or is it to apply no filters at all?

Thanks very much

Omar

[Alexander Dobin]

Hi Omar,

intron motifs: 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT

Only 1,2 are truly canonical.

All parameters in STAR have default values, which are used if not specified.