Tophat2 error when mapping using -G option

Question

[debitboro]

Hi all,

I try to map my PE reads to a specific hg reference, I explain:

1- I retrieved the reference hg from Ensembl (both the .fa and the .gtf file)

2- Since I want to map my PE reads only to [chr1-chr10], I do the following:

 2-1- Extract the [chr1-chr10] from the gtf file
 2-2- filter the resulted gtf file from rRNA
 2-3 add "chr" to the second column of the gtf file, so the final gtf file is file.gtf

3- Building index with bowtie2-build

4- Mapping using Tophat2 including -G option:

tophat2  -p  12  -o  tophat_out  -G  /path/to/the/gtf/file.gtf  /path/to/the/bowtie/index/prefix  my_reads_R1.fq  my_reads_R2.fq

I do all of this in order to get rid of rRNA in the mapping, but I still get the following error:

[2016-04-25 16:45:40] Building Bowtie index from hg_chr1_chr10.fa
    [FAILED]
Error: Couldn't build bowtie index with err = 1

Some help ?