Entering edit mode
3.0 years ago
samuel0325
•
0
Hi i am trying to load genome from file at IGV.
First i sorted that file (Homo_sapiens.GRCh37.75.gtf --> Homo_sapiens.GRCh37.75.sorted.gtf). Second i indexed that file (Homo_sapiens.GRCh37.75.sorted.gtf --> Homo_sapiens.GRCh37.75.sorted.gtf.idx) Third i tried to load genome from file with Homo_sapiens.GRCh37.75.sorted.gtf
But I keep getting message "Could not create index file"
I googled it but i could not get proper answer. Can you help me please?
how did you sort the file ? how did you indexed the file ? can you write in the directory ?
I used igvtools at the igv interface(sort & index both) Both file were in same directory after finished it.
Thank you for reply!!!!
Can you not use
hg19
genome provided (can be downloaded) in IGV itself?I can use that genome but I am trying to use specific genome version. Thank you GenoMax! :)
I wonder if sorting the GTF file messed up the header (depending on how you did the sort, can you clarify?). Have you tried to load the non-sorted file (it should already be in order I would think).
Edit: Use one of the GTF sort tools mentioned in this thread if you had not used a proper sorting tools meant for GFF/GTF files.