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Hi,
I see that CLAP is designed to run on eukaryote genomes.
How to adapt it to run on bacteria?
I changed `make_annotation.sh` by adding species _escherichia_coli_k_12_ and adjusted ftp site and…
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The GRCh38_UCSC2ensembl.txt file is missing contig mapping from the hg38 UCSC side. In using this file to remap UCSC contigs to Ensembl the map fails because of missing contigs.
For example, `chr1…
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@arnikz, I had a look at the RDF and was looking for gene resources... @Chris-Evelo told me that he and Barend had particularly in mind for @JonathanMELIUS to make link sets, so I am exploring what li…
egonw updated
7 years ago
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PTPRC and CD45 refer to the same gene P08575.
In cpdb both names are used in different files, in liana only PTPRC.
Can or does this cause problems?
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Dear Authors,
Thank you for this great tool!
I have been testing CrossMap with DBSNP v151 data and found one type of conversion that doesn't look correct.
For DBSNP rs202079816: given chr22:…
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Dear Doctor，
I used a VCF file that mixed 400 samples to distinguish the source of cells. The script ran without any issues, but did not produce a result file that could be judged. I would like to …
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I'm getting a barf-out when my VCF has an N in the ALT allele:
Command:
``` bash
topiary --mhc-cons --vcf ./test.vcf --output-csv 12n_test.csv --mhc-alleles B46:01 --ic50-cutoff 500 --mhc-epitope-l…
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Hi Jessica and Arthur,
In GlyGen we have protein and glycan data for medically important virus species like SARS-CoV, and HCV. We are planning to submit the data for these species however the protein…
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### Description of feature
Currently the workflow uses the VEP cache for annotation, but should also enable using local files from databases for annotation. Hence, other database sources can be added…
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The following error occurs while trying to download and prepare "Gene expression" data for "TCGA-LIHC". I have many possible old versions like "TCGAbiolinks_2.10.5" that works for my PI and others as…