Hi Everyone

I am trying to make bowtie 1 indexes using hg19.fa and ERCC.fa

First I merged together the two gtf files

hg19 gtf file = "genes.gtf" to the ERCC92.gtf file to get "hg19_GTF_with_ERCC.gtf"

I then merged the two .fa files

command:

cat ERCC92.gtf genes.gtf > hg19_GTF_with_ERCC.gtf
cat ERCC92.fa hg19.fa > hg19_with_ERCC.fa

I then ran bowtie-build command to get the indexes for hg19_with_ERCC

Command:

bowtie-build hg19_with_ERCC.fa hg19_with_ERCC
ls

hg19_GTF_with_ERCC.gtf
hg19_with_ERCC.fa
hg19_with_ERCC.1.ebwt
hg19_with_ERCC.2.ebwt
hg19_with_ERCC.3.ebwt
hg19_with_ERCC.4.ebwt
hg19_with_ERCC.fa

I don't seem to get the .rev.ebwt files everyone seems to get!

Also when I try running tophat alignment

tophat \
  --bowtie1 \
  -p 8 \
  -o Spikes_Test_hg19_ERCC -G /BOWTIE1_ERCC_hg19/hg19_GTF_with_ERCC.gtf \
  /Genomes/ERCC_spike_in_1/BOWTIE1_ERCC_hg19/hg19_with_ERCC \
  /HiSeq23/Sample_A08/Sample_A08_CAGAGAGG-GCGTAAGA_L006_R1_001.fastq.gz \
  /HiSeq23/Sample_A08/Sample_A08_CAGAGAGG-GCGTAAGA_L006_R2_001.fastq.gz

I get the following error:

Error: Could not find Bowtie index files

Does anyone know alternatively where can I find bowtie indexes already built from a hg19 with ERCCs?