Hi, thanks for the useful FreePSI tool to calcaulate PSI value! I have some questions, they might have been covered in the publication or previous issues (exon bed file #7), but it would be great if you reply again here:
What is the format of the ‘exon boundary’ file? I read that it has to be in bed12 format but I have a few specific questions:
Can it have multiple rows for a gene corresponding to separate transcript id or is it compulsory to have only one row per gene?
Can it have overlapping exons from multiple transcripts or do we need to merge them?
Does it make sense to use FreePSI for calculating PSI value of a partial exon instead of the full exon? For example, instead of including coordinates of a full exon from transcriptome annotation, can we include regions within the exon to compare psi values of the start of the exon vs the end of the exon?
Can FreePSI be used for comparing the psi values for the same exon from two different samples? Is there any normalisation needed to account for different sequencing depths between samples? Here is an example using SUPPA
Similar to the above question, can we directly compare psi values of two different exons in the same sample? Does it take into account the lengths of the exons?
Hi, thanks for the useful FreePSI tool to calcaulate PSI value! I have some questions, they might have been covered in the publication or previous issues (exon bed file #7), but it would be great if you reply again here:
Can FreePSI be used for comparing the psi values for the same exon from two different samples? Is there any normalisation needed to account for different sequencing depths between samples? Here is an example using SUPPA
Similar to the above question, can we directly compare psi values of two different exons in the same sample? Does it take into account the lengths of the exons?
I appreciate your time!
Best, Sarang