New to Bowtie

[jjk]

I am pretty new when it comes to bioinformatics. But i need to use bowtie to do only one thing for me. I have multiple tags in a fasta file and i would like to align this against a genome.

Already made an index of my genome of interest, single alignments like:

./bowtie -a -v 2 chloroplast --concise -c ATGCA

works fine...

Now i would like to load a fasta file and run it through the program.

The command:

/bowtie -S chloroplast reads/input.fa chloroplast5000.sam

Does not work because i use an input.fa file and not FASTQ. I obtain all my tags through fasta files and would like to use them directly.

Can someone briefly explain what commands to use?

Thanks a lot!

### I shall keep you updated on the progress ###

This command seems to work:

./bowtie -S chloroplast -f reads/input.fa chloroplast5000.sam

# reads processed: 193
# reads with at least one reported alignment: 147 (76.17%)
# reads that failed to align: 46 (23.83%)
Reported 147 alignments to 1 output stream(s)

[Ben Langmead]

This command seems to work:

./bowtie -S chloroplast -f reads/input.fa chloroplast5000.sam

# reads processed: 193
# reads with at least one reported alignment: 147 (76.17%)
# reads that failed to align: 46 (23.83%)
Reported 147 alignments to 1 output stream(s)

Yes, that's how to do it.

Thanks,
Ben

[jjk]

Tablet

For the people who don't know what to do with the .sam files like i did in the beginning. I found this program

http://bioinf.scri.ac.uk/tablet/

From the Plant Bioinformatics Group SCRI - Tablet

This is available for:

Windows (32 bit) or Windows (64 bit)
Linux (32 bit) or Linux (64 bit)
Apple Mac OS X
Solaris (Sparc)