I'm trying to map some paired- end reads of the sheep up to the reference genome.
So, I have generated the index by using the following command:
bowtie2-build oviAri3.fa oviAri3_bowtie
The files that are created:
oviAri3_bowtie.1.bt2, oviAri3_bowtie.2.bt2, oviAri3_bowtie.3.bt2, oviAri3_bowtie.4.bt2, oviAri3_bowtie.rev.1.bt2, oviAri3_bowtie.rev.2.bt2
So far, everything seems to be ok
Now, I'm trying to do the mapping with the following command:
bowtie2 oviAri3_bowtie -1 BH1_GCCAAT_L001_R1_001.fastq.gz.p -2 BH1_GCCAAT_L001_R2_001.fastq.gz.p BH1_GCCAAT_L001_PE_bwt.sam
The program exits with the message:
No index, query, or output file specified!
unfortunately I cannot find what I'm doing wrong.
Thank you very much in advance,
The bowtie version that I'm using is the latest one: 2.2.4