Couldn't build bowtie index with err = 1
Previous discussions suggests these
- use both refenrece genome and gtf from the same source
- issue can be with terminology “chr#1” in fasta and “1” in gtf
We have tried previously suggested options, but none seems to be useful in the context.
P.S: We are analysing Anophele stephensi (not so general species of anopheles) and vectorbase being the source.
Thank you for all suggestions and comments !!
Command: tophat2 -p 7 -T -G ../../anapholes_stephensi/reference/stephnsi.gtf -o tophat_gtf_out/ ../../anapholes_stephensi/reference/stephensi 1_cutadapt.fastq 2_cutadapt.fastq