GSNAP error

[aaron.odell]

I am trying to run gsnap on RNA seq data and I receive the following error
"Unexpected error. Using IIT_read code on a version 1 IIT"

Here is the command I ran

gsnap -t 16 -N 0 -m .06 -A sam --quality-protocol=illumina -s refGene.gtf -D GSNAP -d hg19 myFastq > output.sam

Does anyone know how to correct this error
I built the genome using gmap_build and did not receive any errors. However, I am unsure that the fasta file I used was in the correct format. Any help would be appreciated

-Aaron

[wendy_cityu]

Have you figured out the reason? I am now facing with the same error.

[aaron.odell]

My error was because the "-s" flag takes an IIT file instead of a gtf. If you look in the README file that came with GSNAP there is a whole section that tells you how to convert the gtf to the proper format. There are two built in GSNAP programs that you need to run before you can map to your genome/transcriptome. They are "gtf_splicesites" and "iit_store"
Hope this helps

-Aaron

[wendy_cityu]

Yes, I just solved in that way, too. Thanks for the reply, though.