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MaveDB allows users to specify accession numbers from major genomic databases (Ensembl, RefSeq, UniProt) when depositing a target sequence. As we develop a validation framework for these accession num…
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I downloaded refseq database and run kaiju for taxonomic assignment of sample DRR496098 downloaded from SRA, in the kaiju/bin directory using the command below;
./kaiju -t ../../kaiju_db/nodes.dmp -f…
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I am unable to buildDB, initially I suspected it was because the fna files were gunzipped but after un-gzipping them, a new issue arose.
I used the following commands to download a smaller version …
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Hi,
How may I fix this run error for executing the _S. cerevisiae_ test case, using your `LTRpred`?
BTW, the 1st test with Hsapiens_ChrY_ltrpred input completed without any error or warning me…
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Hello
I have two viral contigs of approximately 3500bp from the same region of a genome. The two contigs differ by just 1%. Virsorter is run as:
virsorter run -w test.out -i test.fa --min-length 150…
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how can i make file like 'hg19.RefSeq.union.bed.gz', in my case, species is mmu/rno? thans
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There is a difference in the result between refseq and ensembl and I'm not too sure why.
Basically when the genome build is GRCh38 and transcript_set is 'refseq', the variant `11-5248232-T-A` it s…
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Hello eNet developer,
I use the hg38 reference.
How to prepare the hg38_refSeq.Rdata?
Or, can you provide the file in data directory?
Thanks!
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Could add a mapping of Ensembl transcript IDs to NCBI RefSeq ID(s?).
In the Perl API:
```
my @dbentries = @{ $transcript->get_all_DBEntries() };
```
On the db entry: `dbname()` to get the name …
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Ask Jim; apparently we can't match RefSeq IDs letter by letter