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Running MAKER2 pipeline with Augustus for the first time -- need some guidance

genome latest gene annotation augustus maker2 written 3.5 years ago by voidnyx • 10 • updated 5 months ago by Biostar ♦♦ 20

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Maker2 restart after crash

genome annotation maker2 written 13 months ago by sukyi • 0 • updated 13 months ago by genomax ♦ 63k

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Augustus/Maker2 failing due to invalid nucleotides in sequence

augustus assembly maker2 annotation written 18 months ago by harishk0201 • 20

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Recent Replies

C: Uneven PCR in RNA-seq Preparation by genomax ♦ 63k
As long as they are treating all of your samples identically it may be ok. You will need to be mi...
C: How to generate a stripplot like this in Python or R? by steve • 1.9k
in R you can just make a scatter plot in something like ggplot2. You could use facets per gene.
C: Problem installing HTSeq on Windows 10 by makwana.kd • 0
Thank you ATpoint, I have installed it on Ubuntu.
C: Problem installing HTSeq on Windows 10 by makwana.kd • 0
Thank you Jared, Yes I missed that. I instead have installed it on Ubuntu. However, I am getting ...
A: % of change and log2 fold change (L2FC)? by Wuschel • 110
[calculate fold change (FC)][1] When comparing these log transformed values, we use the quotient ...
C: RNAseq sample never as A in last base by lieven.sterck ♦ 4.1k
If I understood correctly that last (extra base) does not get trimmed because it's 'rescued' by t...
A: Uneven PCR in RNA-seq Preparation by biostar.anon • 0
Yes while it is true that there's a protocole, I am currently in contact with a sequencing facili...
C: Why 50bp Illumina run produces 51bp long sequencs? by lieven.sterck ♦ 4.1k
reviving an old post to quickly add a "For future reference/users" message: If your data has b...
C: Estimate gene expression data by Kevin Blighe ♦ 39k
You would have to construct a regression model with some training data. With a model constructed,...
C: RNAseq sample never as A in last base by i.sudbery ♦ 4.0k
Thanks. Quality trimming didn't remove this, but I'll have a go at hard trimming the last base. N...
A: RNAseq sample never as A in last base by lieven.sterck ♦ 4.1k
Yes, I'have seen that before as well (at least for DNA reads). It's a typical pattern for the rea...
C: Estimate gene expression data by banerjeeshayantan • 80
Hi Kevin. I am still in the process of going through recently published materials on the topic (w...

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