bowtie2- running command problem

Question

[vasilislenis]

Hello,

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,

Vasilis.

ps The bowtie version that I'm using is the latest one: 2.2.4

Answer 1

[iraun]

Try this:

bowtie2 \
  -x oviAri3_bowtie \
  -1 BH1_GCCAAT_L001_R1_001.fastq.gz.p \
  -2 BH1_GCCAAT_L001_R2_001.fastq.gz.p \
  -S BH1_GCCAAT_L001_PE_bwt.sam

You need to specify the index with -x and the output with -S.

[vasilislenis]

It seems that its running :)

Thank you very much!