From A List Of Gene Symbols To A Bed File With Tss Position

Question

[Ido]

Hi Biostars!

I have a list of gene symbols (in excel or txt file) and I would like to get a BED file containing all the TSS positions of that list. How can I do that?

Thanks

[simranmaggo]

Thanks Ashutosh,

Is it possible to output a file with genes, location and known variants from genome browser?

[Ashutosh Pandey]

How many genes you are talking about? If it is a large number then downloading the dbSNP data and then using bedtools to intersect it with a gtf file will be much easier. Otherwise you can try Biomart (ensembl.org/biomart/). Under Attributes you can select Variation and in the Filters section you can give a list of genes that you are interested in.

[tanni93]

Hi I am having the same issue but when I "paste list" of my inputs, I am getting errors. This is the format for my gene list

Acat2
Adrb2
Ankrd26
Anxa8
Apcdd1
Arhgap19
Arl4a
Atf3
Auts2
Bdkrb2
Cacna1c
Caly
Casp7
Ccdc15
Cdh13
Cdkn3
Cebpd
Celsr1
Cep70
Chaf1b
Chst3
Cks2
Clec11a

[A. Domingues]

Could you please post the error message? Without that information is is nearly impossible for anyone to help you.

Answer 1

[Ashutosh Pandey]

Try this command: I am assuming that you want the TSS for hg19. Change it to mm10 in the command below if you are working on mouse.

mysql \
  --user=genome \
  -N \
  --host=genome-mysql.cse.ucsc.edu \
  -A \
  -D hg19 \
  -e "select ensGene.name, name2, chrom, strand, txStart, value from ensGene, ensemblToGeneName where ensGene.name = ensemblToGeneName.name"

OR

Go to this link

http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=364666683 (This will take you to the table browser of UCSC genome browser)

To get the TSS based on Ensembl Genes set the following:

• clade: Mammal
• genome: Human
• assembly: hg19
• group: Genes and Gene Prediction
• track: Ensemble Genes
• table: ensGene
• region: genome
• identifiers (names/accessions): (paste or upload list)
• output format: selected fields from primary and related tables (Here you can select fields that you are interested in)

Click "get output"

Check the fields that you want to be displayed (here are some that I would select)

• name Name of gene
• chrom Reference sequence chromosome or scaffold
• strand + or - for strand
• txStart Transcription start position

Click "get output"

[saswati.s2010]

Hello Ashutosh. Can you tell me a way to find out the gene name if I have the TSS and the orthoDB ID?