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Hi Dr. Charles Murphy,
Thank you for developing AGFusion and making it publicly available.
I would like to use agfusion for ensembl >v95, and it seems
**1. I will have to build the database …
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Hi I try to run filter_vep but I got an error
my command is :
```
cd NAS/InfoGene/Rachele/data/VEP_output/
mkdir -p filtered_for_predpathogenic
for chr in {1..22}; do
filter_vep …
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Robel can you share a script which can generate the mapping between uniprotkb_canonical_ac and ensembl_gene_id as a csv file for all organisms in GlyGen, including the ones that will be added in the f…
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Hello,
I have converted my fasta file and paired end reads to make a GTF file using augustus. However, when I am trying to index the fasta file (the gtf file is needed) I recieve an error. This error…
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Hi!
Our analysis and the design of Scout, for historical reasons, heavily rely on CADD. However, there are now several new in silico prediction tools available. The advantage of CADD is that …
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Hello,
Thank you for all your help. We didn't go through any problem since last time untill now with the following command:
```basg
!mkdir -p /staging/tur/Erythroid_Final/outs/qc
!pycistopic t…
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https://asia.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000136250;r=7:36512941-36724494;t=ENST00000617537
Web page Reports that the sequence is 2385 bases long
Ensembl API is in…
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I made a strange observation. When I see the PlasmoDB gene Database, I see that there are `5254` genes but when using Biomart, I get only `4903` genes. Various characterized genes such as `"PBANKA_010…
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Ebsembl is problematic because each species has its own database with their own gene symbol name that needs to be manually identified. To be as smooth as homologene, I need to translate any possible N…
oganm updated
5 years ago
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Hello, I would like to see which specific exons undergo alternative splicing for these genes. Taking SE.MATS.JCEC as an example, I’m currently using the Ensembl website to examine all transcripts of t…