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rank10
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Comment: C: GFF3 to GTF problems
... And then I needed to edit the Gff slightly and now I am stuck again. I can get the genepred file and even a gtf file but popoolation won't read it. I tried to change things in such a way as to prevent a problem from emerging but failed. ...
written 1 day ago by rank10
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Answer: C: GFF3 to GTF problems
... 1. I downloaded a gff file from a close relative to my study organism uploaded by a friend to Genbank. 2. I manually edited the MITOS output gff in BBEdit to match the format in the Genbank gff. Then I deleted the duplicate records for the RNA molecules, while keeping the record 'gene ...
written 1 day ago by rank10 • updated 1 day ago by genomax87k
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Comment: C: GFF3 to GTF problems
... In the end, I worked with AGAT, gffread, and Kent's tools to get the gtf. I had to simplify the gff to get one of them to work properly, and once I had a version that would run, I was able to add complexity back to the gff and then convert to gtf. ...
written 2 days ago by rank10
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Comment: C: GFF3 to GTF problems
... Thank you I got it installed that way ...
written 2 days ago by rank10
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Comment: C: Unable to install samtools in macOS Catalina
... Worked great for a while. Now I find myself having to reinstall it every time I want to use it. ...
written 3 days ago by rank10
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GFF3 to GTF problems
... Dear All, my ultimate goal is to use the genewise option in popoolation to evaluate allele frequency variation at mitochondrial snps between two divergent populations. I need to convert the gff file to a gtf file first. So I have buried myself in different ways of annotating the GFF3 file to get po ...
agat poolseq gffread popoolation mitos written 6 days ago by rank10 • updated 6 days ago by h.mon30k
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Comment: A: Unable to install samtools in macOS Catalina
... I set up Conda etc based on the Biostars manual. I did this in April. I have tried several ways to get samtools to work, and it does not work. I have seen that others have this problem, but I have not been able to track the route to a solution. Please help! errors below: Downloading and Extra ...
written 12 days ago by rank10 • updated 12 days ago by Istvan Albert ♦♦ 84k

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