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?
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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 -
Matlab's BioMap class has a write method that creeates SAM and BAM files.
HTH
L.Comment
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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.Comment
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