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In order to use VEP, I made an AUGUSTUS GFF annotation file. Here you can see the GFF structure for the first gene:
```
SuperScaffold AUGUSTUS gene 1 5061 0.02 - . …
eprdz updated
10 months ago
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Hello.
I am trying to use CLEAR for my data set and running the following command:
clear_quant -1 /userdata/sharmishtha/Hela/trimmedFastqFiles/trim_HeLa-AMT-1_R1.fastq.gz -2 /userdata/sharmishtha/H…
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The `PANCAN_mutation` dataset ([online doc](https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/?dataset=TCGA.PANCAN.sampleMap/PANCAN_mutation&host=https://tcga.xenahubs.net)) contains several…
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I was looking at the gene annotation files, in particular, http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/annotation_set/CHM13.v2.0.gff3
It looks like the file contains multiple problems, mostly to…
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I've tried performing a multiplication operation with integers (Int[N]) of different bit lengths and encountered an error. It seems that operations between different bit lengths are not currently supp…
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Thank you for the great package and easy to follow instructions.
I've managed to run through the tutorial with my own non-model genome now.
Is there a tool to automatically codon optimise a desi…
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Hi,
Sorry for this basic level question, I am still a novice with bioinformatics.
When I attempt to run 3UTR_orf_20170816.pl as:
perl 3UTR_orf_20170816.pl -i test.fa -d /home/hayden/Downloads/E…
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Hi
How FATE decide the biotype of each hit?
I could not find the description of the criteria for "blue/yellow/red" in the 9th column.
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Mikado pick generates a metrics file for the final models (mikado.loci.metrics.tsv) and for the input models (mikado.subloci.metrics.tsv and mikado.monoloci.metrics.tsv). The mono and sunbloci files d…
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I have been using mitochondrial annotation to teach prokka to a master class very successfully for the last few years - the mtDNA annotates very successfully and very fast so that the students can see…