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JY-Zhou / FreePSI

An alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome
GNU General Public License v3.0
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exon bed file #7

Open ArashDepp opened 2 years ago

ArashDepp commented 2 years ago

Hi, I have two questions regarding the exon bed file. Would appreciate your time and help in this.

  1. Should I provide non-overlapping disjoint exons for a gene OR all the exons from gencode gtf file would work (which often overlap at their boundaries)?

  2. In case I provide only the non-overlapping intervals for a gene, will free PSI infer other possible isoforms having exons with different ends than the provided bed files?

Best.

JY-Zhou commented 2 years ago

Sorry for my delayed reply, and appreciate your interest in FreePSI. :)

For the first question, FreePSI can only deal with non-overlapping disjoint exons for a gene. If there are overlapped exons, I suggest preprocessing the annotation files into non-overlapping exons. This preprocessing can always work, e.g. if A and B are overlapped, it can be represented as A, A∩B, B. This script can help you to do the preprocess: scripts/mergeToFlatGene.py.

For the second question, the answer is no. FreePSI only estimates PSI value for the provided non-overlapping exons. However, if you have some potential regions that might be new exons, you can directly add these regions to the annotation file, and check the estimated PSI values for these regions. (Note that FreePSI doesn't care about the composition of isoforms.)

Hope this would help, and really sorry for my late reply.

ArashDepp commented 2 years ago

Hi. Got it. Thanks for helping me with this. I will post in case I have any more concerns. Best regards.

On Sun, Mar 13, 2022 at 10:07 AM Arrows @.***> wrote:

Sorry for my delayed reply, and appreciate your interest in FreePSI. :)

For the first question, FreePSI can only deal with non-overlapping disjoint exons for a gene. If there are overlapped exons, I suggest preprocessing the annotation files into non-overlapping exons. This preprocessing can always work, e.g. if A and B are overlapped, it can be represented as A, A∩B, B. This script can help you to do the preprocess: scripts/mergeToFlatGene.py https://github.com/JY-Zhou/FreePSI/blob/82830c5df94d33fe9e0df4054905e4c3bb47b381/scripts/mergeToFlatGene.py .

For the second question, the answer is no. FreePSI only estimates PSI value for the provided non-overlapping exons. However, if you have some potential regions that might be new exons, you can directly add these regions to the annotation file, and check the estimated PSI values for these regions. (Note that FreePSI doesn't care about the composition of isoforms.)

Hope this would help, and really sorry for my late reply.

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