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7.3 years ago
morovatunc
▴
550
Hi,
I have obtained Repeatmasker bed file for hg19 assembly via UCSC table browser. But I have seen that they are quite common across genome. Is there any wiki or something that I can get the information about th meaning of that annotation.
For example; I could only get this link related with this info. But it is not very informative. —> www.repeatmasker.org/cgi-bin/ViewRepeat?id=LTR40a —> LTR40a
Let this graduate student have a happy new years eve.
Best regards,
Tunc.
What kind of information are you looking for?
As far as I know, the repeatmasker database is the definitive resource on repeats. If you want more detail, you would probably need to dig into the literature. But characterising repeats has not been popular for many years so information tends to be pretty thin.
I am working on an effect of transcriptional factor binding on transcriptional activity. I have a bunch of regions where I see this TF binding. But I would like to filter out the binding regions where for example bind on a highly repetitive region. therefore, I wanted to ask in my question that is there a specific annotation tag in repeat masker database which I assume those binding events are trash.
Thank you for your answer
In that case, I would filter out all annotated repeats without worrying about specific tags.
LINEs, SINEs and LTRs are most common in the assembled genome but the DNA/RNA/Simple repeats are also problematic in ChIP-seq (mapping issues etc.)
Having said that, I would also set a limit on the degree of overlap between your TF and a given repeat before tossing it out. It's best to eyeball a few regions to set this definition but something around 50% might work. For example, if your peaks are 300 bp, only exclude if >150 bp overlaps a repeat. Otherwise you might throw away a lot of peaks where the repeat overlap is incidental.
Or you could do the inverse and only select for peaks that overlap a gene.
Thank you very much for your extended answer. It will really help me a lot!
Best regards,
Tunc.