Questions tagged [exon]

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Find the genomic locations of exons of certain human gene

So I know Consensus CDS has the genomic locations of exons, however, only of the exons in the CDS. Everything before or after is not included. NIH variation viewer has those (kinda-) radio buttons ...
1
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0answers
17 views

Downloading exon-wise gene sequence using commandline

I want to download exon-wise gene sequence of around 200 genes from NCBI. Is there anyway to do this from terminal? I have the transcript id for each sequence and I am using efetch command to download ...
0
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0answers
19 views

What is the tP statistic from ANGSD?

We were looking for genetic diversity in the exon level of an MHC transcript. We used ANGSD to calculate Thetas, Tajima and Neutrality tests and one of the thetas was a pairwise theta, however I am ...
0
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0answers
38 views

Coding vs non-coding DNA length

I am trying to calculate the total exonic length (in bp) in order to see where the coding-noncoding ratio of roughly 1% to 99% comes from. We know all chromosomes total about 3 billion base pairs. So ...
3
votes
1answer
196 views

Pipeline for extracting gene from multiple genomes for use in HyPhy selection analyses?

I have been trying to obtain some preliminary data from HyPhy selection analyses to inform a larger project. I have obtained a number of assembled mammalian genomes from NCBI with the initial goal of ...
1
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2answers
62 views

Get gene exons from UCSC browser by HGNC name

I have a set of gene names in HGNC standard and I want to get all their exons (in BED format) from the UCSC browser but it seems like the browser doesn't index genes by their HGNC name. How can I do ...
6
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3answers
764 views

Can exons be located outside of the coding sequence?

I have a gff file like this (I edited the name): ...