Bowtie beginner question...

[milesgr]

I am trying to perform an alignment of a fastq file using bowtie.

bowtie -q -p 8 -v 3 -a -m 600 --best --strata /inputfolder/inputFILE.fq

I get the following error:
No query or output file specified!

I also tried the following:
bowtie -q /inputfolder/inputFILE.fq -p 8 -v 3 -a -m 600 --best --strata

and received the same message.

I'm not sure what I am doing wrong but I feel like it's something very simple. Any help would be greatly appreciated.

[DZhang]

Hi milesgr,

Did you prepare the index files for Bowtie? You need to specify the base in the command.

Douglas

https://www.contigexpress.com

[milesgr]

Thanks for the quick response...I originally forgot to include the index (so I fixed that), but I did have a build of it already. One more question...

I built the script to run by (see the below script) changing folders to the folder containing the scripts, which is writable. I then (below this) call bowtie using the full path, referencing the index file (in index_folder) and the fastq file (in folder fastqpath). Neither index_folder or fastqpath are writable folders. My question is, to which folder will the output file be attempted? I assumed it was the working directory, but I wanted to make sure. Furthermore, if I wanted the output file to go to a different folder, how would I accomplish this? Thanks.

cd script_directory

/full_path/bowtie -q -p 8 -v 3 -a -m 600 --best --strata /index_folder /fastqpath/fastqfile.fq

[DZhang]

Your current command, as is, will print the output to the screen. Check the bowtie online manual on the "output" session; it has many options for its output. As to redirect the output to a different directory, just specify the path to it and make sure the directory is already there (and as you are already aware, writable).

Douglas

https://www.contigexpress.com

[milesgr]

I read up on this and I guess my last (hopefully) question is:

If I add the --sam as shown below, this should output to a sam format, correct? Further, when you specify, "As to redirect the output to a different directory, just specify the path to it and make sure the directory is already there.", what do you mean just specify the path to it? Where would I place that specification?

/full_path/bowtie -q -p 8 -v 3 -a -m 600 --best --strata --sam /index_folder /fastqpath/fastqfile.fq

Say, for instance I wanted to output the .sam file to /home/temp, could you do me a favor and put that in the command so I could see an example of this? Thanks again for all your help...I really appreciate it.

[DZhang]

/full_path/bowtie -q -p 8 -v 3 -a -m 600 --best --strata --sam /index_folder /fastqpath/fastqfile.fq > /home/temp/bowtie_out.sam

[chaomeizhang]

batch bowtie alignment

Firstly I must say I am a new to the linus and bowtie.

My questions are
1 I did demultilexing using CASAVA, and got a bunch of fatsq.gz files, then I did unzip of all the files. Should I do the alignment with bowtie file by file individually or write a loop or use a batch file to do the alignment?

2 After I get the alignment, may I come back to use the CASAVA? or I had better to use the downstream softwares such as Myrna (paper) ,TopHat (paper), Cufflinks (paper),RNASEQR (paper).

many thanks in advance.