Have you seen such base distribution plot in BS-seq?
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If by BS-seq you mean Bisulfite Sequencing I have to say NO. Conversion has failed or all Cs were methylated! -
I concur with nucacidhunter and add "Yikes, that's bad!"Comment
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If the experiment is 2x125bp paired-end sequencing and both were concatenated into this one plot and the sequencing is non-directional and you used some kind of target enrichment technique or random primed pull-down then there might be a chance that there is something to be had from the data. But only you would know your library that well...
If this is not the case, I would like to agree with the above posters.
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This plot indicates a very high level of adapter dimer fragments in your library. Filter these out with your favorite trimming/filtering tool and then repeat the base composition plot to see what your valid library fragments look like.Comment
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