I have a number of DNA sequences. Each sequence is either up or downstream of an SNP. How can I compute the presence of transcription start site from it? Thanks for your insight.
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You could map your sequences to a model genome assembly (e.g., hg38 for human genome, etc.) with a tool like Bowtie2, which recovers intervals where those sequences map, and associate them with genomic annotations like Gencode, Ensembl, CAGE, etc. using a tool like BEDOPS bedmap, which can give you strand and offsets from which to derive the position of the TSS within the original input sequence.
Thanks for insisting on BEDOPS. The sequences I have are a result of mapping with hg38. I'm having a hard time finding the TSS determined in cerebellum, prefrontal cortex, temporal cortex tissues. Would appreciate if you could help me with that.
Not a problem at all, glad to help!
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What is the organism your working on....??
Welcome to biology, where we do appropriate experiments to deduce features like this, and where not everything can simply be computed.
Experimentally speaking, can I use an already identified dataset of TSS containing its locations and accordingly check if it falls within the range of my dna sequences?
Yes - but ideally you would use TSS determined in your tissue of interest as this level of regulation can be dependent on the cell type.
I'm interested in the brain tissues. Which folder here contains that information?