I have 2 samples, paired end RNA sequence from illumina. I have done the QC and trimming.
Now after trimming with trimgalore I have
A_R1.val_fq A_R2.val_fq B_R1.val_fq B_R2.val_fq
Now I performed tophat for genome mapping. I ran this command
tophat -p4 -G GRCh38_latest_genomic.fna -o tophat_result bowtie_index A_R1_val.fq
but its throwing this error.
[FAILED] Error: Couldn't build bowtie index with err = 1
I have a genome annotation file:
gencode.v43.chr_patch_hapl_scaff.annotation.gtf and a reference genome:
GRCh38_latest_genomic.fna. I tried making a bowtie index by using this command :
bowtie2-build GRCh38_latest_genomic.fna bowtie_index
This gave me files like this:
bowtie_index.1.bt2 bowtie_index.2.bt2 bowtie_index.3.bt2 bowtie_index.4.bt2 bowtie_index.rev.1.bt2 bowtie_index.rev.2.bt2
Please help me on this step. I could not figure out where I am doing mistake.