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I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads.

After the BAM filtering steps, I used the Scallop results with TransDecoder. Next, I used bamCoverage to create RNA-Seq profile. I noticed that not always the first isoform is the best one compared to the RNA-Seq profile as could be seen below a few examples:

1. Screen Shot 2020-08-22 at 4 35 26 PM

2. Screen Shot 2020-08-22 at 4 38 45 PM

3. Screen Shot 2020-08-22 at 4 51 37 PM

4. Screen Shot 2020-08-22 at 4 58 42 PM

5. Screen Shot 2020-08-22 at 5 04 34 PM

By any chance, is there a way to keep only the best isoform which is in red box?

Thank you in advance,

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  • $\begingroup$ I'm not familiar with Scallop/TransDecoder, but it would be helpful to know what you mean by "best". I think I agree with you about which one is "best" but formulating a specific quantitative definition of "best" would be a good first step. Is there any definition of "best" in these tools? How would they evaluate what is "best"? $\endgroup$
    – Maximilian Press
    Aug 31, 2020 at 17:08
  • $\begingroup$ Unfortunately, the additional information was too long to post them on this side, Therefore, I posted them here $\endgroup$
    – user977828
    Sep 3, 2020 at 5:14

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