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Greeting everyone
I got this partially sequenced genome from a plant in Cyperaceae family (using Illumina) and I’m trying to find repetitive sequences in it. I got like 100.000 scaffolds and I used Tandem Repeats Finder to get only the ones containing tandem repeats (which still is a lot of scaffolds), but there is still a lot to do manually.
I need to find repetitive sequences with enough base pairs to create a primer for it and with a representative amount of repetitions, so I’ve been going scaffold to scaffold (those Tandem Repeat Finder gave me) looking for them. I was hoping there was a program out there that could do this for me automatically (essentially look for tandem repeats with X base pairs and Y repeats). A friend in bioinformatics recommended me this forum but I’m kind of a bioinfo virgin, so any help is appreciated!
I got this partially sequenced genome from a plant in Cyperaceae family (using Illumina) and I’m trying to find repetitive sequences in it. I got like 100.000 scaffolds and I used Tandem Repeats Finder to get only the ones containing tandem repeats (which still is a lot of scaffolds), but there is still a lot to do manually.
I need to find repetitive sequences with enough base pairs to create a primer for it and with a representative amount of repetitions, so I’ve been going scaffold to scaffold (those Tandem Repeat Finder gave me) looking for them. I was hoping there was a program out there that could do this for me automatically (essentially look for tandem repeats with X base pairs and Y repeats). A friend in bioinformatics recommended me this forum but I’m kind of a bioinfo virgin, so any help is appreciated!
Thanks in advance
SamBR90.
(BR stands for Brazil so sorry about the lazy english
)
SamBR90.
(BR stands for Brazil so sorry about the lazy english
)