Is there a comprehensive reference for all the STRs (Short tandem repeats) present in human genome? I looked into few different resources but couldn't get all the repeats in hg38.
For example, I downloaded UCSC simple repeats annotated by Tandem Repeat Finder (http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/simpleRepeat.txt.gz), but the list misses serval repeats. I downloaded another reference called gangSTR (https://github.com/gymreklab/GangSTR#references) and this one misses some repeats too. There was only about 30% overlap between the 2 databases.
On a slightly different note, I noticed the shortest repeat region length (not repeat unit length) in hg38.simpleRepeat.txt.gz was 25. So any repeat region less than 25 bases are not included in them.
Thanks!
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Could you give examples of some missed repeats? It isn't clear how you're defining what is missed
Thank you! For example these regions are not found in the repeat databases -
CHR START STOP SEQ Repeat_Unit Repeat_times
chr1 930278 930287 GGCGGCGGC GGC 3
chr1 939279 939288 CTGCTGCTG CTG 3
chr1 942602 942610 GCGCGCGC GC 4