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RNA seq and promoter consensus sequence

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

rna-seq
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updated by shoujun.gu shoujun.gu • written by kanwarjag kanwarjag

1 answer

  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

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written by shoujun.gu shoujun.gu

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