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CDS length for each human gene

Is there a way to retrieve ENSEMBL IDs from a search query?Converting Ensembl Gene IDs to Entrez Gene IDs through biomartIdentifying relevant SNPs from a listCounting the number of paralogues for mouse genes gives me the wrong frequency in RA good tool for gene locus visualizationDownload proteomes from NCBI based only on binomial namesGet Gene Expression Matrix from GEOqueryFinding gene length using ensembl IDFinding gene name from human genome using SP1 transcrition factor binding site from Postion Weight MatrixRetrieve RNA sequencing data for human p53 colon cancer cell lines

1

$begingroup$

Does anyone know where and how could I download a list of all human genes and the length of the coding sequence for each gene? Is it possible to do this on the NCBI site, ensembl?

gene sequence-analysis ncbi ensembl

share|improve this question

edited 2 days ago

Kamil S Jaron

3,057942

asked Apr 30 at 14:52

solimanelefantsolimanelefant

1083

New contributor

solimanelefant is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

$endgroup$

• 
  
  
  

  
  2
  

  
  
  
  
  
  

  
  $begingroup$
  Which coding sequence? I mean, do you just want whichever has been designated the 'canonical' transcript or do you want all possible isoforms?
  $endgroup$
  – terdon♦
  Apr 30 at 14:54
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Hi terdon, thanks for the quick reply! Yes exactly, the canonical transcript is good enough!
  $endgroup$
  – solimanelefant
  Apr 30 at 14:56
  
  

  
  
  
  


• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  Michael G. suggests to take a look at relevant front-end, NCBI's eFetch. Which is supposedly perfect for what you need.
  $endgroup$
  – Kamil S Jaron
  2 days ago
  

  
  
  
  

add a comment | 

1

$begingroup$

Does anyone know where and how could I download a list of all human genes and the length of the coding sequence for each gene? Is it possible to do this on the NCBI site, ensembl?

gene sequence-analysis ncbi ensembl

share|improve this question

edited 2 days ago

Kamil S Jaron

3,057942

asked Apr 30 at 14:52

solimanelefantsolimanelefant

1083

New contributor

solimanelefant is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

$endgroup$

• 
  
  
  

  
  2
  

  
  
  
  
  
  

  
  $begingroup$
  Which coding sequence? I mean, do you just want whichever has been designated the 'canonical' transcript or do you want all possible isoforms?
  $endgroup$
  – terdon♦
  Apr 30 at 14:54
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  Hi terdon, thanks for the quick reply! Yes exactly, the canonical transcript is good enough!
  $endgroup$
  – solimanelefant
  Apr 30 at 14:56
  
  

  
  
  
  


• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  $begingroup$
  Michael G. suggests to take a look at relevant front-end, NCBI's eFetch. Which is supposedly perfect for what you need.
  $endgroup$
  – Kamil S Jaron
  2 days ago
  

  
  
  
  

add a comment | 

$begingroup$

Does anyone know where and how could I download a list of all human genes and the length of the coding sequence for each gene? Is it possible to do this on the NCBI site, ensembl?

gene sequence-analysis ncbi ensembl

share|improve this question

edited 2 days ago

Kamil S Jaron

3,057942

asked Apr 30 at 14:52

solimanelefantsolimanelefant

1083

New contributor

solimanelefant is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

$endgroup$

share|improve this question

edited 2 days ago

Kamil S Jaron

3,057942

asked Apr 30 at 14:52

solimanelefantsolimanelefant

1083

New contributor

solimanelefant is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

share|improve this question

edited 2 days ago

Kamil S Jaron

3,057942

asked Apr 30 at 14:52

solimanelefantsolimanelefant

1083

New contributor

solimanelefant is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

edited 2 days ago

Kamil S Jaron

3,057942

edited 2 days ago

Kamil S Jaron

3,057942

asked Apr 30 at 14:52

solimanelefantsolimanelefant

1083

New contributor

solimanelefant is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

asked Apr 30 at 14:52

solimanelefantsolimanelefant

1083

2 Answers
2

active

oldest

votes

4

$begingroup$

While I haven't found a way to limit the results to the canonical transcript only, you can get a list of genes, transcripts and their CDS lengths using Ensemble's BioMart. I have already set it up for you, you can see the results, and modify them, here (click on the "Results" link if you don't see them).

Essentially, you just need to go to BioMart, and

1. select "Ensembl Genes 96" (the number will change if the version changes) as the database and "uman Genes" as the dataset.




2. Click on "Filters", and set Gene type to coding and Transcript type to protein_coding.




3. From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures".

share|improve this answer

edited Apr 30 at 22:23

answered Apr 30 at 15:48

terdon♦terdon

4,9702830

$endgroup$

add a comment | 

0

$begingroup$

Ensembl has an FTP site that allows you to select and download only the coding sequences from many different genomes.
https://useast.ensembl.org/info/data/ftp/index.html

To determine the length of those sequences, download the associated gtf or gff3 annotation file. The annotation file is tab delim. The fourth and fifth column represent genomic loci of the annotated region. Subtract the amount in the fourth column from the amount in the fifth column to yield the length of all the annotated features.
You can easily do this in R after loading the file in the environment using the Magrittr library. The following code will create a new column called gene_length with the associated gene lengths.

install.packages("magrittr")
# this only needs to be done once
library(magrittr)
# must be run each time the library is neaded
annotation.gtf <- read.table("path/to/annotation.gtf")
annotation.gtf$start <- annotation.gtf[,4]
annotation.gtf$end <- annotation.gtf[,5]
annotation.new-column.gtf <- annotation.gtf %>%
 mutate(gene_length=end-start)

share|improve this answer

edited 2 days ago

Kamil S Jaron

3,057942

answered 2 days ago

Drew J-HDrew J-H

12

New contributor

Drew J-H is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

$endgroup$

add a comment | 

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4

$begingroup$

While I haven't found a way to limit the results to the canonical transcript only, you can get a list of genes, transcripts and their CDS lengths using Ensemble's BioMart. I have already set it up for you, you can see the results, and modify them, here (click on the "Results" link if you don't see them).

Essentially, you just need to go to BioMart, and

1. select "Ensembl Genes 96" (the number will change if the version changes) as the database and "uman Genes" as the dataset.




2. Click on "Filters", and set Gene type to coding and Transcript type to protein_coding.




3. From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures".

share|improve this answer

edited Apr 30 at 22:23

answered Apr 30 at 15:48

terdon♦terdon

4,9702830

$endgroup$

add a comment | 

4

$begingroup$

While I haven't found a way to limit the results to the canonical transcript only, you can get a list of genes, transcripts and their CDS lengths using Ensemble's BioMart. I have already set it up for you, you can see the results, and modify them, here (click on the "Results" link if you don't see them).

Essentially, you just need to go to BioMart, and

1. select "Ensembl Genes 96" (the number will change if the version changes) as the database and "uman Genes" as the dataset.




2. Click on "Filters", and set Gene type to coding and Transcript type to protein_coding.




3. From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures".

share|improve this answer

edited Apr 30 at 22:23

answered Apr 30 at 15:48

terdon♦terdon

4,9702830

$endgroup$

add a comment | 

$begingroup$

While I haven't found a way to limit the results to the canonical transcript only, you can get a list of genes, transcripts and their CDS lengths using Ensemble's BioMart. I have already set it up for you, you can see the results, and modify them, here (click on the "Results" link if you don't see them).

Essentially, you just need to go to BioMart, and

1. select "Ensembl Genes 96" (the number will change if the version changes) as the database and "uman Genes" as the dataset.




2. Click on "Filters", and set Gene type to coding and Transcript type to protein_coding.




3. From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures".

share|improve this answer

edited Apr 30 at 22:23

answered Apr 30 at 15:48

terdon♦terdon

4,9702830

$endgroup$

share|improve this answer

edited Apr 30 at 22:23

answered Apr 30 at 15:48

terdon♦terdon

4,9702830

answered Apr 30 at 15:48

terdon♦terdon

4,9702830

answered Apr 30 at 15:48

terdon♦terdon

4,9702830

0

$begingroup$

Ensembl has an FTP site that allows you to select and download only the coding sequences from many different genomes.
https://useast.ensembl.org/info/data/ftp/index.html

To determine the length of those sequences, download the associated gtf or gff3 annotation file. The annotation file is tab delim. The fourth and fifth column represent genomic loci of the annotated region. Subtract the amount in the fourth column from the amount in the fifth column to yield the length of all the annotated features.
You can easily do this in R after loading the file in the environment using the Magrittr library. The following code will create a new column called gene_length with the associated gene lengths.

install.packages("magrittr")
# this only needs to be done once
library(magrittr)
# must be run each time the library is neaded
annotation.gtf <- read.table("path/to/annotation.gtf")
annotation.gtf$start <- annotation.gtf[,4]
annotation.gtf$end <- annotation.gtf[,5]
annotation.new-column.gtf <- annotation.gtf %>%
 mutate(gene_length=end-start)

share|improve this answer

edited 2 days ago

Kamil S Jaron

3,057942

answered 2 days ago

Drew J-HDrew J-H

12

New contributor

Drew J-H is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

$endgroup$

add a comment | 

0

$begingroup$

Ensembl has an FTP site that allows you to select and download only the coding sequences from many different genomes.
https://useast.ensembl.org/info/data/ftp/index.html

To determine the length of those sequences, download the associated gtf or gff3 annotation file. The annotation file is tab delim. The fourth and fifth column represent genomic loci of the annotated region. Subtract the amount in the fourth column from the amount in the fifth column to yield the length of all the annotated features.
You can easily do this in R after loading the file in the environment using the Magrittr library. The following code will create a new column called gene_length with the associated gene lengths.

install.packages("magrittr")
# this only needs to be done once
library(magrittr)
# must be run each time the library is neaded
annotation.gtf <- read.table("path/to/annotation.gtf")
annotation.gtf$start <- annotation.gtf[,4]
annotation.gtf$end <- annotation.gtf[,5]
annotation.new-column.gtf <- annotation.gtf %>%
 mutate(gene_length=end-start)

share|improve this answer

edited 2 days ago

Kamil S Jaron

3,057942

answered 2 days ago

Drew J-HDrew J-H

12

New contributor

Drew J-H is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

$endgroup$

add a comment | 

$begingroup$

Ensembl has an FTP site that allows you to select and download only the coding sequences from many different genomes.
https://useast.ensembl.org/info/data/ftp/index.html

To determine the length of those sequences, download the associated gtf or gff3 annotation file. The annotation file is tab delim. The fourth and fifth column represent genomic loci of the annotated region. Subtract the amount in the fourth column from the amount in the fifth column to yield the length of all the annotated features.
You can easily do this in R after loading the file in the environment using the Magrittr library. The following code will create a new column called gene_length with the associated gene lengths.

install.packages("magrittr")
# this only needs to be done once
library(magrittr)
# must be run each time the library is neaded
annotation.gtf <- read.table("path/to/annotation.gtf")
annotation.gtf$start <- annotation.gtf[,4]
annotation.gtf$end <- annotation.gtf[,5]
annotation.new-column.gtf <- annotation.gtf %>%
 mutate(gene_length=end-start)

share|improve this answer

edited 2 days ago

Kamil S Jaron

3,057942

answered 2 days ago

Drew J-HDrew J-H

12

New contributor

Drew J-H is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

$endgroup$

install.packages("magrittr")
# this only needs to be done once
library(magrittr)
# must be run each time the library is neaded
annotation.gtf <- read.table("path/to/annotation.gtf")
annotation.gtf$start <- annotation.gtf[,4]
annotation.gtf$end <- annotation.gtf[,5]
annotation.new-column.gtf <- annotation.gtf %>%
 mutate(gene_length=end-start)

share|improve this answer

edited 2 days ago

Kamil S Jaron

3,057942

answered 2 days ago

Drew J-HDrew J-H

12

New contributor

Drew J-H is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

edited 2 days ago

Kamil S Jaron

3,057942

edited 2 days ago

Kamil S Jaron

3,057942

answered 2 days ago

Drew J-HDrew J-H

12

New contributor

Drew J-H is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.

answered 2 days ago

Drew J-HDrew J-H

12