Where can I not download hg38 annotation file in txt format? Can somebody point me toward web site? I need basic text file with just a chromosome-start-stop-gene name. Illumina offers .gz format. I downloaded a txt.gz. file and can not open it. http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html?langsel=/ch/
the .gz file probably didn't download completely.
here you go https://www.ebi.ac.uk/ena/data/view/GCA_000001405.27
Hi,
You could also use the annotation of ENSEMBL - https://www.ensembl.org/info/data/ftp/index.html
You can find all the information you need here.
Hope this helps.
Thank you all for your suggestions.
I downloaded one file: refGene.txt from Illumina web site:
https://fts.illumina.com/download.html#/mail/
There are No headers in the file:
I see chromosome #, I see the strand -/+,
I see gene identifier (gene name?),
I need a gene start and gene stop positions, but I see multiple other columns. Which one is gene start and stop?
1278. NM_001286451 | chr15 | - + 90930917 | 90932569 | 90931274 | 90932540 4 90930917,90931703,90932054,90932428, | 90931405,90931944,90932110,90932569, | 0
Irina St Louis Try browsing the chromosome annotations from the EBI website
https://www.ebi.ac.uk/ena/data/view/GCA_000001405.27
I looked at the "Regions" file, attached . It contains the identified regions with accession numbers, and the ranges of these sequences
cheers
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