How to pipe Bowtie's commands

[Fad2012]

Dear all

How can i pipe the following bowtie's commands so the terminal on mac would run them all at once

bowtie-build mainseq.fasta build
bowtie -S build -f -I 20 -X 7500 -a -m 1 -v 3 --rf -1 reads_1.fasta -2 reads_2.fasta aligned.sam
samtools view -bS aligned.bam aligned.sam
samtolls sort aligned.bam aligned.sorted
samtools index aligned.sorted.bam

Many thanks for your help.

[sdarko]

bowtie2 -x $your_ref -U $in | samtools view -bSu - | samtools sort - $out

That's how I do it.

[mastal]

put the commands in a shell script and run the shell script.

you have to have bowtie and samtools installed on your Mac and added to your path.

use a text editor to create a file called something like 'run_bowtie.sh'.

put something like '#!/bin/bash' or whatever shell you are using, as the first line of the script,

paste the rest of the commands into the file and save it.

then run it from the terminal window.

$./run_bowtie.sh

[Fad2012]

Thanks mastal, it has worked.

Thanks sdarko, it has not worked, it seems i should use bowtie2 to ge it worked.

I am still wondering if piping would work as efficient as creating a small bash program, which has worked perfectly with me as mastal has suggested.

Many thanks

[Fad2012]

Sorry, i should have mentioned that i had to use the following code to add executable permissions to the bash shell file to work:

chmod u+x run_bowtie

Then you can run it as mentioned by mastal:
./run_bowtie

[EGrassi]

I am still wondering if piping would work as efficient as creating a small bash program, which has worked perfectly with me as mastal has suggested.

In theory a pipe avoids writing all the intermediate results to the disk thus is more efficient, sadly it is not always possible/easy to combine different tools with pipelines.

[sdarko]

Thanks sdarko, it has not worked, it seems i should use bowtie2 to ge it worked.

I am still wondering if piping would work as efficient as creating a small bash program, which has worked perfectly with me as mastal has suggested.

I think this would work for bowtie:

bowtie -S -f -I 20 -X 7500 -a -m 1 -v 3 --rf build -1 reads_1.fasta -2 reads_2.fasta | samtools view -bSu - | samtools sort - aligned.sorted

I generally generate bash scripts that use piping to be most efficient so as to not make intermediate files.