I am new to gene alignment. I am trying to align few short/long reads with a reference genome using bwa software. I have been following this tutorial - https://icb.med.cornell.edu/wiki/index.php/Elementolab/BWA_tutorial
I did the following -
- Downloaded bwa-0.5.9.tar.bz2 and build.
- Downloaded reference human genome as wg.fa
- Created bwt index using - bwa index -p hg19bwaidx -a bwtsw wg.fa.
- Try and align long reads from 454seqs.txt - bwa bwasw hg19bwaidx 454seqs.txt > 454seqs.sam
The output (SAM format) file of alignment only has the header information and no alignment information. Can someone guide me if I am missing something. Also, what would be the next steps in your opinion to play around with this software to get a better understanding of the run times for alignment.