.cmap file in Bioscope

[Erika Feltrin]

Hello all,

I am analyzing a bacterial genome.
I am running the Find Small InDels analysis with Bioscope and it requires the .cmap file as an input file. I am not able to find where is this file. After the secndary analysis, I am supposed to find this file somewhere in my cluster or shoud I prepare it by myself?
Does anybody try to do that?

Thanks
Erika

[bpetersen]

The cmaps we are using for bioscope consist of three columns:
1: number of chromosome (1-25)
2: chromosome name (chr1, chrM etc.)
3: path to fasta sequences of the single chromosomes
Hope this helps!

[Erika Feltrin]

Thanks bpeterson,

the problem is that we have just one chromosome since we are analyzing bacterial strain reads.
Should I put just one line in my .cmap file referring to the only chromosome I have?

[bpetersen]

I haven't worked with using only one reference, but I think you should just give it a try. I can't see why it shouldn't also work.

[westerman]

I have used one-line cmaps for bacterial work. Note that the columns must be separated by tabs, not spaces.

[Erika Feltrin]

Thanks,

I have done a one-line .cmap file and it worked.

Cheers
Erika