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2.5 years ago
Alireza.Tafazoli
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0
Hi, I'm looking for any shell script which may provide the Y chromosome structure information, gene names, number of repeated/duplicated genes, STRs list, etc. via Terminal. Can anybody help me with that?
Your question is unclear. Why do you need a script? It sounds like what you need is data - specifically annotation data, probably ib BED or GFF format. Please explain.
Something like GFF but containing information about repeated areas too. The scripts can be manipulated for getting different/extra features too. Also. I can share it with other staff in different centers easier.
Still not sure I understand. Are you looking for repeat annotation tools, say like EDTA?
Not exactly. Actually, I found many information that I was looking for in Biomart Ensemble but there was no data about repeated sequences there. As you know, we have some genes and STRs which are repeated along chromosome Y. I would like to know how many genes and markers are there. How many times they are repeated. etc. I would expect a tool which may provide all of this and give me (for example a csv file) as an output.