Chromosomes names need to start whith "chr"

[fvnieuwe]

Dear David,

My input file looks like this (it is a Bismark coverage2cytosine format originating from a non-model organism):
Fvb1 4 + 1 0 CG CGA
Defiant is not recognizing this file format because defiant requires that chromosome names start with "chr".

I changed read_bisulfite_data.h (and recompiled) to get Defiant going on my input file:
if ((number_of_columns == 1) && (strstr(temporary_char_string,"chr") != NULL)) {
into
if (number_of_columns == 1) {
This workaround works and Defiant is generating relevant results in no time!

However, to make the annotation work using a gtf file that contains chromosome names not starting with "chr", more elaborate changes are needed.

It would be great if Defiant could be used on non-model organisms.

Thanks!

Kind regards,
Filip

[bio15anu]

Hey,
I am also running into this problem. Additionally I've found that even when appending "chr" to the beginning of the chromosome names, defiant is shortening them to 5 characters and thus making them unusable for me.

It would be really nice to remove this restriction!

Cheers,
Adam

[hhg7]

Hi @bio15anu

I have adjusted defiant so it uses longer chromosome names, and uploaded defiant.zip to GitHub. Please let me know if the change works better for you.

-Dave