Here's a simple question...I have a list of gene names that I want to retrieve a GTF file of those genes specifically. I put the list into UCSC for RefSeq genes and download the GTF file. The resulting GTF files does NOT contain the gene names, only the gene id's. So, how do I get a GTF file with the gene names???
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by golharam View PostHere's a simple question...I have a list of gene names that I want to retrieve a GTF file of those genes specifically. I put the list into UCSC for RefSeq genes and download the GTF file. The resulting GTF files does NOT contain the gene names, only the gene id's. So, how do I get a GTF file with the gene names???
A sample output for the Actb gene in mouse looks like this:
Code:chr5 mm10_refFlat stop_codon 142903798 142903800 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142903801 142903941 0.000000 - 0 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142903116 142903941 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142904067 142904248 0.000000 - 2 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142904067 142904248 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142904344 142904782 0.000000 - 0 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142904344 142904782 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142905237 142905476 0.000000 - 0 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142905237 142905476 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat CDS 142905564 142905686 0.000000 - 0 gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat start_codon 142905684 142905686 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142905564 142905692 0.000000 - . gene_id "Actb"; transcript_id "Actb"; chr5 mm10_refFlat exon 142906652 142906724 0.000000 - . gene_id "Actb"; transcript_id "Actb";
Hope this helps!
Dario
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
Yesterday, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 06:57 AM
|
0 responses
9 views
0 likes
|
Last Post
by seqadmin
Today, 06:57 AM
|
||
Started by seqadmin, Yesterday, 07:17 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
Yesterday, 07:17 AM
|
||
Started by seqadmin, 05-02-2024, 08:06 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-02-2024, 08:06 AM
|
||
Started by seqadmin, 04-30-2024, 12:17 PM
|
0 responses
23 views
0 likes
|
Last Post
by seqadmin
04-30-2024, 12:17 PM
|
Comment