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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
The text was updated successfully, but these errors were encountered:
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!
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
The text was updated successfully, but these errors were encountered: