Questions tagged [exon]

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6 votes
3 answers
1k views

Can exons be located outside of the coding sequence?

I have a gff file like this (I edited the name): ...
Cleb's user avatar
  • 743
4 votes
1 answer
333 views

On the same strand, for the same gene, can exons be overlapping?

I want to get a set of exon regions for each protein coding gene. I extracted a set of relevant information (chromosome, start, end, gene ID, gene name, gene type, exon number and exon ID) from a GTF ...
gc5's user avatar
  • 1,783
4 votes
0 answers
46 views

How to summarize multiple exon copy numbers into copy number of the corresponding gene

I have a matrix, sample by exon, containing a copy number value for each pair (sample, exon). I would like to generate a second matrix, sample by gene, where the copy number of the exons is ...
gc5's user avatar
  • 1,783
3 votes
1 answer
387 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 ...
PollardMD's user avatar
2 votes
1 answer
62 views

Availability of information on genes in Gnomad VCF data

I was wondering does the gnomad genome data that is downloaded in the vcf format on variants contain information on what is the nearest gene and is the genomic location available exome/intron? if yes ...
agnesa rivkin's user avatar
2 votes
2 answers
140 views

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 ...
mrPuzzle's user avatar
2 votes
0 answers
19 views

Calculate interval of flanking introns

I am looking for a easy way to calculate the intervals of flanking introns based on a transcript annotation file. I have chosen a very complicated method: ...
serbe204's user avatar
1 vote
2 answers
2k views

Extract only exon regions from GFF/GTF file with input bed regions

I have a bed file that contains a list of regions and I would like to extract only the exon regions from a GTF/GFF file that are contained in the given regions. Is there a simple command or tool that ...
SBDK8219's user avatar
  • 195
1 vote
2 answers
88 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 ...
Paghillect's user avatar
1 vote
2 answers
126 views

What is the tP statistic from ANGSD?

We were looking for genetic diversity in the exon level of an MHC transcript and analysing the data under ANGSD (Analysis of next generation Sequencing Data) written in C++ We used ANGSD to calculate ...
mk894's user avatar
  • 105
1 vote
0 answers
92 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 ...
Saumya Gupta 1910110's user avatar
0 votes
0 answers
46 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 ...
janeu's user avatar
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