I could not load GTF data at IGV("Could not create index file") Please help me :)
0
0
Entering edit mode
5 months 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?

gtf igvtools igv sort index • 875 views
ADD COMMENT
1
Entering edit mode

how did you sort the file ? how did you indexed the file ? can you write in the directory ?

ADD REPLY
0
Entering edit mode

I used igvtools at the igv interface(sort & index both) Both file were in same directory after finished it.

Thank you for reply!!!!

ADD REPLY
1
Entering edit mode

Can you not use hg19 genome provided (can be downloaded) in IGV itself?

ADD REPLY
0
Entering edit mode

I can use that genome but I am trying to use specific genome version. Thank you GenoMax! :)

ADD REPLY
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 1725 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6