circos plot problem

Question

[mauryaneha57]

hello everyone, i am new to circos and i am trying to plot the circos graphs. I tried with the basic ones it worked for me but i am not getting what is segdup.txt file if someone knows please describe what are these files. and their format through some example.

Answer 1

[Kevin Blighe]

Hello,

segdup.txt just contains co-ordinates of segmental duplications in a genome. A segmental duplication is a type of repeat also known as low copy repeat (LCR). As you know, the mammalian genome in particular has evolved to be quite 'fluid' and has a messy maintenance system, which has actually benefited us. Segmental duplications and other types of repeats have served to create new genes and promote diversity of function of the human proteome and transcriptome.

Here is a direct link to a sample segdup.txt on the CIRCOS github page: https://raw.githubusercontent.com/vigsterkr/circos/master/data/5/segdup.txt

segdup00001 hs1 465 30596

segdup00001 hs2 114046768 114076456

segdup00002 hs1 486 76975

segdup00002 hs15 100263879 100338121

segdup00003 hs1 486 30596

segdup00003 hs9 844 30515

segdup00004 hs1 486 9707

segdup00004 hsY 57762276 57771573

segdup00005 hs1 486 9707

segdup00005 hsX 154903076 154912373

segdup00006 hs1 486 9707

When you draw segmental duplications on CIRCOS, a curved line will be drawn to connect the genomic regions that are assumed to be such duplications.

Kevin