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Hi,
I am running BiasAway in a human dataset. tes_background_hsapeins.fa is coming from random fragments of 1000bp (done with bedtools). The TE_set_reference_hg38.fa is a compendium of 4million tra…
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I run the SalmonTE like this:
./SalmonTE.py quant --reference=hs ./example/CTRL_1_R1.fastq
and get error as below:
![image](https://user-images.githubusercontent.com/34944811/34442783-659b468…
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Welcome buddies,
Looks like we're a team for hackseq 17 to work on bioSyntax. Welcome! Let's start with some brief introductions?
My name is Artem, I'm a grad student at UBC in Genetics. I'm (main…
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Transposable Elements (TE) and Repeat Regions (RE) do not have 'exons', and thus no child elements for those annotations; is this the reason why the 'Details' panel in the bottom half of the 'Annotato…
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I had Funannotate working great before, but for some reason now when I try to use funannotate predict it crashes right towards the end, complaining it can't find predict_results/genome.gff3. The direc…
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Dear Jon,
I have launched funannotate predict with the following parameters, and it has failed:
```
funannotate predict -i 901.masurca.scf.fasta -o 901.fun_out --species "Linum usitatissimum" -…
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1. Difficult to choose msga parameters for large haplotypes
2. Difficult to get out a standard "vcf" file, summarizing msga graph
3. How do I name the chromosomes (impacts #2)
Code below
``…
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Dear Jon,
I looked thoroughly at my previous funannotate results (derived a month ago) and found that **funannotate-p2g.py** seems to fail. As a result, finally, out of 500,000 proteins, tblastn ha…
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Hi Jon,
EVM finished properly, but now the scripts complains about the tRNA scan. I guess is someting about compilation but I am not sure
```
2017-04-29 06:11:13,499: 126,950 total gene models f…
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Hi Zhang,
I am able to use AGOUTI with one bam file.
How can I use multiple bam files simontaneously?
Tao