May it would be easier for you to use the "Table Browser" and download the annotations as e.g. BED file. You can find an explanation of this format here:
Gene Start Stop
Hi! I am trying to extract start and stop positions for a gene list. Can someone suggests and files for homo sapiens that can be downloaded from which I can parse the info using perl? I know UCSC has files like knowngene and refgene but I am not sure about the formatting in those txt files. Any suggestions?
• 3,977 views
•
link
updated
by
seidel
•
written
by
bioinformatics123 •
•
written
by
bioinformatics123 •
2 answers
Click the button called "describe table schema" and it will tell you what is in each column.
• 0 views
•
link
written
by
Istvan Albert
You might also try ensembl biomart. Given that you already have a gene list, ensembl has a web front-end you could use to extract the information you need, and you likely wouldn't have to use perl to parse out the results. You can select the fields you would like returned in a text file (i.e. start, stop).
Log in to answer this question.
More posts like this
-
Downloading full list of Homo sapiens genes
written by Nigussie •
-
Parsing gene expression value for a list of genes from GEO
written by Natasha •
-
Extracting multiple features using NCBI's e-utilities?
written by ThePresident
-
cruzDB coordinates vs UCSC coordinates
written by nkinney06 •
-
GRCh38 Annotation for non coding RNA (e.g. miRNA)
written by Aurelie MLB
-
Ensembl Gtf Cuffmerge Duplicates
written by andrew.j.skelton73
-
Gencode Annotation In Refgene Format
written by Phil S.
-
Read 2 Files Perl
written by bioinformatics123 •
-
Where Can I Get Annovar 'Refgene' Format?
written by jessada •
-
Fasta Format Of Chromosomes And Biopython
written by Ma
