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Questions related to output gtf file. #8

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linglingtingfei opened this issue Jan 21, 2019 · 2 comments
Open

Questions related to output gtf file. #8

linglingtingfei opened this issue Jan 21, 2019 · 2 comments

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@linglingtingfei
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linglingtingfei commented Jan 21, 2019 •
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Hi @yangao07 ,
I run the program successfully. But in the output file, I found that there is something weird(shown on the screenshot below).

  1. Why the position of the transcripts is 0？

  2. Why do some transcripts split into two parts?

Hope you can help solve these issues. I'd really appreciated that.

qq 20190121120156
qq 20190121120307222
@yangao07
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It is weird to see those lines in the output file.
So sorry about this.

Can you upload a small test input file that could result in those lines in the output?

Yan

@linglingtingfei
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Hi @yangao07 ,
Thank you for your reply. I upload a file from a human sample. It seems that lr2rmats can't handle reads with poor MAPQ and then split one read into two parts. By the way, this result only show on 'samp1.novel.gtf' file.

samp1_long_test.txt

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@yangao07 @linglingtingfei