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Problem with gtf file #42
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@LiuJJ0327 Thanks for reporting the bug. I have updated the master branch to |
I tried latest version, but new error exist. Please see below. Has loaded transcripts from 25 Chromosomes/Scaffolds |
Can you check if your gft file has the same chromosome id as is in your bam file? The typical theme here in one file you have |
I tested using: strawberry test.bam -o test_out.gtf -g hg19_sed.gtf -p 8 https://drive.google.com/file/d/1muxvaxDc3ZGMG0pR-e2iTVvlBUMkNLfT/view?usp=sharing |
@LiuJJ0327 Again, thanks for sharing the test data. After awhile, I found out this corner case is causing the problem
As you can see, a gene is located on two different chromosomes. I fix this issue in v1.1.2. I have tested the new version on your input data and it works fine. |
@LiuJJ0327 Does the new version work for you? |
Yes. Thank you so much. |
Hi, I downloaded hg19 gtf file from UCSC gene brower and used -g option in strawberry, however I get the same problem as issue #20
error information:
strawberry: /root/strawberry/src/alignments.cpp:1859: double compute_doc(uint, uint, const std::vector&, std::vector&, IntronMap&, uint): Assertion `gf.right() >= gf.left()' failed.
I saw it may caused by a one bp intron in the gtf file and has been fixed in 0.9.3. However I implement the latest version 1.1.1 and still had this problem.
Can you give me any idea?
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