SSRs abundance calculation

Question

[moohit21]

Hi everybody, I have a .misa file and i want to calculate abundace of classes of ssrs from that misa file, for example in dinucelotide repeats which one is repeating maximum time and same in tri, tetre,penta and hexanucleotides. is there any software or any script which can count this?

Thanks in advace for the help.

[Nitin Narwade]

Do you want the abundance of repeat sequence or abundance of mono, di, tri, tetra etc repeats (not sequences just length of repeat)?

If you are interested in the abundance of the length of repeats then it's pretty simple. There is one column SSR type in which p1 means mono-nucleotide repeat p2 means di-nucleotide and so on. So open the file in excel and make a pivot table of SSR type column you will get repeat lengthwise abundance.

Answer 1

[Tm]

When you run misa.pl on your scaffold file, two files are generated:

1. .misa file
2. .statistics file

So you can get different types of repeats along with the times they appeared in .statistics file

[sruthi]

Hey, I tried running a FASTA file in MISA using the below command:

misa.pl file.fasta

and it says

Use of uninitialized value $total in concatenation (.) or string

How do I troubleshoot this? It would of great help if someone could help me out on this.

TIA