Hi,
I can run the code some days ago . But cant run now.
Problem 1: Output is ok
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
utr5 = getSequence(chromosome=3, start=185514033, end=185535839,
type="entrezgene",seqType="5utr", mart=ensembl)
Output :
5utr entrezgene
Sequence unavailable 10644
GGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644
3
GGGGGGCGGAGGAGGAGGAGAGACGAGGGCAGCGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG
10644
CGGAGGAGGCGAGGAGCGCCGGGTACCGGGCCGGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG 10644
No UTR is annotated
for this transcript 10644
Problem 2:Problem is here
protein = getSequence(id=c(100, 5728),type="entrezgene",seqType="peptide",
mart=ensembl)
Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, :
Query ERROR: caught BioMart::Exception::Database: Error during query
execution: Can't create/write to file '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI'
(Errcode: 2)
I need help please.
/.......Tanvir Ahamed
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