Various methods of creating .sam/.bam files

[wmyashar]

I know that there are many great programs out there such as bowtie, galaxy, bioconductor, etc that can do these steps for me but I am interested in creating my own .bam file starting off from a .fastq file. Oh and my main software of choice has been MATLAB which has worked out great for me. I am trying to align this sequence but I am wondering whether there is an option from MATLAB to compare this alignment to one that is provided by NCBI or another websource. On top of this, I feel like MATLAB can map this sequence onto the genome and record the counts of the alignment. The rest of the conversion, however, I am kind of shaky on, has anyone tried this or knows of a better way to approach this?

[adaptivegenome]

If you use matlab to do the alignment as long as you report the alignment according to SAM specs, you can stream that data into samtools and it will produce a BAM. Look up the view command:

http://samtools.sourceforge.net/samtools.shtml

[cetto]

Matlab's BioMap class has a write method that creeates SAM and BAM files.

http://www.mathworks.com/help/bioinfo/ref/biomapclass.html

HTH
L.

[chadn737]

I am confused as to what you are actually doing. Are you trying to map raw data to the genome? Are you even working with next-gen data? You say sequence as if it is singular, so is this perhaps a single sequence you are trying to align?

If you are trying to simply analyze already aligned reads, then that is a different matter.