Hi all,
We have several metagenomic datasets and we are interested in creating fragment recruitement plots. that show the alignment of the reads along the genome and the sequence similarity of the reads compared to the aligned region. For more info see figure 2 in the Plos publication here: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050077
We have already mapped all the metagenomic datasets with bwa against the reference genomes, so running another blast run is a waste of time in my opinion. But the IGV viewer only shows the alignment of the read, but does not show the similarity score for all reads at once.
Any suggestions on how we can tackle this issue?
I think you can plot the MAPping Quality with reads lengths from your sam file to get the same result.
Thanks for you suggestion
I figured out that I could use only a fraction of the metagenome reads which gives me a smaller dataset fro blasting that works just as good.
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