Tag: locus_tag

How to extract genomic upstream region of a protein identified by its NCBI accession number?

How to extract genomic upstream region of a protein identified by its NCBI accession number? 1 I have a list of NCBI protein accession numbers. I would like to extract out the upstream genomic region of the corresponding gene’s nucleotide sequence. I will be thankful to you if you can…

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does not contain a ‘gene’ attribute

htseq-count returns : does not contain a ‘gene’ attribute 1 Dear BIOSTAR community, I’m trying to make count matrix with htseq-count, htseq-count -s yes -t gene -i gene 01.sorted.sam annotation_cattle.gff > 01.txt even with –idattr=gene , it returns error: Error processing GFF file (line 1864255 of file annotation_cattle.gff): Feature gene-D1Y31_gp1…

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Download nucleotide sequence with locus_tag

Download nucleotide sequence with locus_tag 1 I have a list of locus_tag, my idea was to download them using esearch but the downloaded file is not the desired gene, instead the nucleotide sequence of the entire contig is downloaded. in this example my gene of interest to download has 830…

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