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Benson-Genomics-Lab / TRF

Tandem Repeats Finder: a program to analyze DNA sequences
https://tandem.bu.edu/trf/trf.html
GNU Affero General Public License v3.0
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last four column of the output #6

Open gorliver opened 3 years ago

gorliver commented 3 years ago

There are four columns with sequences in the output tabular file. It seems no document about these sequences.

@seq8
35738 35771 16 2.1 16 88 0 50 11 23 0 64 1.26 TTCTTCATCTTTTAAC TTCTTCTTCTTTTTACTTCTTCATCTTTTAACTT AGTAACTGAACGATTATGATTTTACTGTAATATATCTACTACAAGTTTTT TCTCTTTAAATCTCATATGAAGATGATAAAACACATCAATGGAGGAAAGA

I wonder what these sequences are? Thank you.

kcamnairb commented 3 years ago

I am not even able to find documentation on what any of the columns represent.

gorliver commented 3 years ago

I am not even able to find documentation on what any of the columns represent. Some of the columns are documented here: https://tandem.bu.edu/trf/trf.definitions.html

yzhernand commented 2 years ago

Sorry, I'm no longer in Gary's lab so I don't get too many chances to address things in this repo too often.

You're right, those columns are not documented and they should be. They are: the consensus pattern, the repeat sequence, the left flanking sequence, right flanking sequence.

A '.' (dot) for either flanking sequence means there is no sequence in that region (length 0).

yzhernand commented 2 years ago

Also, the rest of the columns are documented in the README on this repo as well: https://github.com/Benson-Genomics-Lab/TRF#table-explanation