My goal is to determine the ratio of raw sequencing reads which produced one contig to sequence reads which formed a different contig.
Using the program Bowtie2, I can map unassembled reads to my contigs of interest. Once I do, I'm left with a Sequence Assembly/Map (.sam) file. I'd like to know the number of reads which map to each residue in a contig. Ultimately, I'd like to be able to say that the sequencer generated ~100x coverage of RuBisCO gene #1, ~200x coverage of RuBisCO gene #2, and ~5000x coverage of 16S genes.
Can anyone recommend a paper where this was done well or a program commonly used?
Using the program Bowtie2, I can map unassembled reads to my contigs of interest. Once I do, I'm left with a Sequence Assembly/Map (.sam) file. I'd like to know the number of reads which map to each residue in a contig. Ultimately, I'd like to be able to say that the sequencer generated ~100x coverage of RuBisCO gene #1, ~200x coverage of RuBisCO gene #2, and ~5000x coverage of 16S genes.
Can anyone recommend a paper where this was done well or a program commonly used?
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