RNA seq and promoter consensus sequence

Question

[kanwarjag]

I have a rat RNA-seq data I want to check in 1000 bp upstream of TSS of these genes a common consensus sequence. Is there ant tool that may help me directly to find TSS from gene list and screen in -1000 bp of TSS to identify consensus sequence.

Thanks

Answer 1

[shoujun.gu]

1. use BioMart or ucsc table browser to get the fasta file: http://www.ensembl.org/biomart/martview/fe3159819bb337fedf76e062da87b913 https://genome.ucsc.edu/cgi-bin/hgTables

2. use homer motif analysis tool to find the common consensus sequence: http://homer.ucsd.edu/homer/ngs/peakMotifs.html