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WGLab / LIQA

Long-read Isoform Quantification and Analysis
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High abundance but no reads #3

Closed mei-du closed 3 months ago

mei-du commented 3 years ago

Hi team, I've run the isoform quantification pipeline and have discovered this issue. Would you be able to help me clarify it? I've attached some screenshots. IGV inputs are the same as the LIQA ones and I used the recommended parameters. Thank you. SAMD11 LIQA example.docx

huyustats commented 3 years ago

Hi team, I've run the isoform quantification pipeline and have discovered this issue. Would you be able to help me clarify it? I've attached some screenshots. IGV inputs are the same as the LIQA ones and I used the recommended parameters. Thank you. SAMD11 LIQA example.docx

Hi, would you mind share the sub dataset for this gene and the reference file you used with me to dig out this issue? Thanks!

mei-du commented 3 years ago

Just shared my repository with you, thanks!

zjzace commented 2 years ago

Hi,

I also got this issue. Some genes/transcripts with high read coverage but no output from LIQA.

huyustats commented 2 years ago

Hi,

I also got this issue. Some genes/transcripts with high read coverage but no output from LIQA.

Thanks for your interests in using LIQA. To my experience, reads mapped to unknown isoforms of the gene may cause this issue. We will figure it out soon.

agouru55 commented 3 months ago

Try running the updated package of LIQA. There is now also a novel isoform detection tool (which you can find on Usage page), which may clarify your issue.