I am trying to get a comprehensive list of simple repeats (mono-, di-, tri-, tetra-) in the human genome (hg19). I have downloaded the simpleRepeat.txt.gz from UCSC, but seems it is missing some of the repeats we are interested in. For example, chr1:981861-981868[CCCCCCCC], chr1:1116223-1116230[GGGGGGGG] are some mono nucleotide repeats we are interested in looking at, but they are not on the UCSC list. Thus, I was trying to generate a list using TRF, but still, some of the repeats I was trying to get did not get reported by TRF, e.g., chr1:981861-981868[CCCCCCCC], with the default parameters. Can someone provide some insights here:
- Is there any place where I can download a really 'comprehensive' simple repeats list from?
- If no to question #1, what would be the best way to curate such a list? Is running tools like TRF or RepeatMasker a good idea?
- If TRF is something you would suggest, how should I make it report these mono-nucleotide repeats that I was missiong with the default parameters?
Thanks
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written
by
Jackie
2 answers
the following C program will find the simple repeats:
compile
gcc biostar267241.c
example:
curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr1.fa.gz" | gunzip -c | ./a.out | grep -E '(981861|1116223)'
chr1 981861 981868 C[7]
chr1 1116223 1116230 G[7]
mono-repeat (same base) of len > 5
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You could download repeats for hg19 from the Repeatmasker folks and convert to BED with convert2bed to do set operations:
$ wget -qO- http://www.repeatmasker.org/genomes/hg19/RepeatMasker-rm405-db20140131/hg19.fa.out.gz | gunzip -c - | convert2bed --input=rmsk - > hg19.fa.out.bed
You could do ad-hoc searches with bedops, piping in your region of interest:
$ echo -e 'chr1\t981861\t981868' | bedops -e 1 hg19.fa.out.bed -
Or pass in a file of regions of interest:
$ bedops -e 1 hg19.fa.out.bed roi.bed > answer.bed
Perhaps you could use this with Pierre's binary to construct results with simple repeats and more complex repeat hits.
Thank you, Alex, that's a great resource, and I have downloaded the repeat masker (RM) file, I think combining the list generated using Pierre's code with this file will give a good starting list.
However, I am still trying to understand why, even this RM file is missing some simple repeats, e.g., a trinucleotide repeat chr1:6680069-6680085 [GAA]n. For those of you who understands RM well, is there some criteria for a simple repeat to be included in the final RM list? e.g., copy number of the unit needs to be >=10, or something like that? as most of these 'longer repeats' are all present in the RM file.
It's unclear to me what parameters were used to generate these files. The best people to ask would probably be the Repeatmasker folks.
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Have you looked at the UCSC Table browser? Check in the group "Repeats". There are multiple options available that you can download the data for.