CDS length for each human geneIs 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
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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
$begingroup$
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
edited May 1 at 7:51
Kamil S Jaron
3,082942
asked Apr 30 at 14:52
solimanelefantsolimanelefant
1083
$endgroup$
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
edited May 1 at 7:51
Kamil S Jaron
3,082942
asked Apr 30 at 14:52
solimanelefantsolimanelefant
1083
$endgroup$
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
May 1 at 7:53
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
edited May 1 at 7:51
Kamil S Jaron
3,082942
asked Apr 30 at 14:52
solimanelefantsolimanelefant
1083
$endgroup$
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
gene sequence-analysis ncbi ensembl
edited May 1 at 7:51
Kamil S Jaron
3,082942
asked Apr 30 at 14:52
solimanelefantsolimanelefant
1083
edited May 1 at 7:51
Kamil S Jaron
3,082942
asked Apr 30 at 14:52
solimanelefantsolimanelefant
1083
edited May 1 at 7:51
Kamil S Jaron
3,082942
edited May 1 at 7:51
Kamil S Jaron
3,082942
edited May 1 at 7:51
Kamil S Jaron
3,082942
3,082942
asked Apr 30 at 14:52
solimanelefantsolimanelefant
1083
asked Apr 30 at 14:52
solimanelefantsolimanelefant
1083
asked Apr 30 at 14:52
solimanelefantsolimanelefant
1083
1083
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
May 1 at 7:53
add a comment |
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
May 1 at 7:53
2
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
$begingroup$
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
$begingroup$
Hi terdon, thanks for the quick reply! Yes exactly, the canonical transcript is good enough!
$endgroup$
– solimanelefant
Apr 30 at 14:56
1
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
May 1 at 7:53
$begingroup$
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
May 1 at 7:53
add a comment |
2 Answers
2
active
oldest
votes
$begingroup$
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
select "Ensembl Genes 96" (the number will change if the version changes) as the database and "uman Genes" as the dataset.
Click on "Filters", and set
Gene typetocodingandTranscript typetoprotein_coding.From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures".
answered Apr 30 at 15:48
terdon♦terdon
4,9902830
$endgroup$
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)
edited May 1 at 13:03
Kamil S Jaron
3,082942
answered May 1 at 11:33
Drew J-HDrew J-H
12
$endgroup$
add a comment |
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2 Answers
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active
oldest
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2 Answers
2
active
oldest
votes
active
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active
oldest
votes
$begingroup$
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
select "Ensembl Genes 96" (the number will change if the version changes) as the database and "uman Genes" as the dataset.
Click on "Filters", and set
Gene typetocodingandTranscript typetoprotein_coding.From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures".
answered Apr 30 at 15:48
terdon♦terdon
4,9902830
$endgroup$
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
select "Ensembl Genes 96" (the number will change if the version changes) as the database and "uman Genes" as the dataset.
Click on "Filters", and set
Gene typetocodingandTranscript typetoprotein_coding.From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures".
answered Apr 30 at 15:48
terdon♦terdon
4,9902830
$endgroup$
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
select "Ensembl Genes 96" (the number will change if the version changes) as the database and "uman Genes" as the dataset.
Click on "Filters", and set
Gene typetocodingandTranscript typetoprotein_coding.From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures".
answered Apr 30 at 15:48
terdon♦terdon
4,9902830
$endgroup$
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
select "Ensembl Genes 96" (the number will change if the version changes) as the database and "uman Genes" as the dataset.
Click on "Filters", and set
Gene typetocodingandTranscript typetoprotein_coding.From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures".
answered Apr 30 at 15:48
terdon♦terdon
4,9902830
edited Apr 30 at 22:23
answered Apr 30 at 15:48
terdon♦terdon
4,9902830
answered Apr 30 at 15:48
terdon♦terdon
4,9902830
answered Apr 30 at 15:48
terdon♦terdon
4,9902830
4,9902830
add a comment |
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)
edited May 1 at 13:03
Kamil S Jaron
3,082942
answered May 1 at 11:33
Drew J-HDrew J-H
12
$endgroup$
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)
edited May 1 at 13:03
Kamil S Jaron
3,082942
answered May 1 at 11:33
Drew J-HDrew J-H
12
$endgroup$
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)
edited May 1 at 13:03
Kamil S Jaron
3,082942
answered May 1 at 11:33
Drew J-HDrew J-H
12
$endgroup$
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)
edited May 1 at 13:03
Kamil S Jaron
3,082942
answered May 1 at 11:33
Drew J-HDrew J-H
12
edited May 1 at 13:03
Kamil S Jaron
3,082942
edited May 1 at 13:03
Kamil S Jaron
3,082942
edited May 1 at 13:03
Kamil S Jaron
3,082942
3,082942
answered May 1 at 11:33
Drew J-HDrew J-H
12
answered May 1 at 11:33
Drew J-HDrew J-H
12
answered May 1 at 11:33
Drew J-HDrew J-H
12
12
add a comment |
add a comment |
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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
May 1 at 7:53