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)
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)
Comment