Question: bowtie2- running command problem
0
gravatar for vasilislenis
4.5 years ago by
vasilislenis100
United Kingdom
vasilislenis100 wrote:

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

reference alignment bowtie2 • 5.9k views
ADD COMMENTlink modified 4.5 years ago by RamRS21k • written 4.5 years ago by vasilislenis100
1
gravatar for iraun
4.5 years ago by
iraun3.5k
Norway
iraun3.5k wrote:

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

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

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by iraun3.5k

It seems that its running :)

Thank you very much!

ADD REPLYlink written 4.5 years ago by vasilislenis100
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