Question

Short Tandem Repeats analysis

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9.1 years ago

marina-orlova ▴ 90

I need to analyze 3 nucleotides tandem repeats, which tool is best in your opinion for this goal?

I looked for this on Biostars but the last answer I managed to find was 2.5years ago. People told about lobSTR and NTRFinder. Are there any new good tools?

tandem-repeats • 2.2k views

ADD COMMENT • link updated 2.4 years ago by Ram 44k • written 9.1 years ago by marina-orlova ▴ 90

Ram · Answer 1 · 2015-11-19

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9.1 years ago

h.mon 35k

What kind of data do you have? Do you have (draft) genome assemblies? Transcriptome assemblies? Anyway, here and here are posts which are somewhat recent, a lot newer than 2.5 years.

I never used lobSTR, but as far as I understand it aims at finding STR on next-generation sequencing data. Is this the kind of data you have?

ADD COMMENT • link 9.1 years ago by h.mon 35k

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Yes, NGS data. hg19 is a reference genome

ADD REPLY • link 9.1 years ago by marina-orlova ▴ 90

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So the only software I am aware is lobSTR.

ADD REPLY • link updated 5.1 years ago by Ram 44k • written 9.1 years ago by h.mon 35k

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thank you for the answer!

ADD REPLY • link 9.1 years ago by marina-orlova ▴ 90