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14 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"

gtf igvtools igv sort index • 1.8k views
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how did you sort the file ? how did you indexed the file ? can you write in the directory ?

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

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

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

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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.