Body: <p>I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads.</p>
  <p>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:</p>
  <p>1.
  <img src="https://user-images.githubusercontent.com/588297/90951101-e1a4ec80-e49a-11ea-8d9d-beea34a26d5e.png" alt="Screen Shot 2020-08-22 at 4 35 26 PM" /></p>
  <p>2.
  <img src="https://user-images.githubusercontent.com/588297/90951106-e9fd2780-e49a-11ea-85ce-6082a39bd110.png" alt="Screen Shot 2020-08-22 at 4 38 45 PM" /></p>
  <p>3.
  <img src="https://user-images.githubusercontent.com/588297/90951109-f41f2600-e49a-11ea-86c4-b61c63a2466d.png" alt="Screen Shot 2020-08-22 at 4 51 37 PM" /></p>
  <p>4.
  <img src="https://user-images.githubusercontent.com/588297/90951113-000ae800-e49b-11ea-85a4-077c77a9d2e3.png" alt="Screen Shot 2020-08-22 at 4 58 42 PM" /></p>
  <p>5.
  <img src="https://user-images.githubusercontent.com/588297/90951118-07ca8c80-e49b-11ea-80ac-421c3f85ca98.png" alt="Screen Shot 2020-08-22 at 5 04 34 PM" /></p>
  <p>By any chance, is there a way to keep only the best isoform which is in red box?</p>
  <p>Thank you in advance,</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-08-31T17:08:33.093Z
Comments.Text: 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"?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-03T05:14:09.700Z
Comments.Text: Unfortunately, the additional information was too long to post them on this side, Therefore, I posted them [here](https://github.com/TransDecoder/TransDecoder/issues/111#issuecomment-685267466)
Comments.UserDisplayName: user977828
Tags: <phylogenetics><sam><sequence-annotation><rna-splicing><isoform>
Title: BAM file filteing to remain best isoform
ThreadText: # BAM file filteing to remain best isoform
  
  (Asked by: username_0 on 2020-08-27)
  
  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](https://user-images.githubusercontent.com/588297/90951101-e1a4ec80-e49a-11ea-8d9d-beea34a26d5e.png)
  
  2.
  ![Screen Shot 2020-08-22 at 4 38 45 PM](https://user-images.githubusercontent.com/588297/90951106-e9fd2780-e49a-11ea-85ce-6082a39bd110.png)
  
  3.
  ![Screen Shot 2020-08-22 at 4 51 37 PM](https://user-images.githubusercontent.com/588297/90951109-f41f2600-e49a-11ea-86c4-b61c63a2466d.png)
  
  4.
  ![Screen Shot 2020-08-22 at 4 58 42 PM](https://user-images.githubusercontent.com/588297/90951113-000ae800-e49b-11ea-85a4-077c77a9d2e3.png)
  
  5.
  ![Screen Shot 2020-08-22 at 5 04 34 PM](https://user-images.githubusercontent.com/588297/90951118-07ca8c80-e49b-11ea-80ac-421c3f85ca98.png)
  
  By any chance, is there a way to keep only the best isoform which is in red box?
  
  Thank you in advance,
  
  **Tags:** phylogenetics, sam, sequence-annotation, rna-splicing, isoform
  
  > **Comments:**
  > **username_1**: 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"?  
  > **username_0**: Unfortunately, the additional information was too long to post them on this side, Therefore, I posted them [here](https://github.com/TransDecoder/TransDecoder/issues/111#issuecomment-685267466)  
  
  ---
  
  ## 0 answers
  
  