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Old 12-03-2015, 06:18 PM   #1
acdan
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Default what an interesting base distribution plot!

Have you seen such base distribution plot in BS-seq?
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Old 12-03-2015, 07:42 PM   #2
nucacidhunter
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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!
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Old 12-04-2015, 12:18 AM   #3
dpryan
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I concur with nucacidhunter and add "Yikes, that's bad!"
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Old 12-04-2015, 02:16 AM   #4
fkrueger
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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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Old 12-04-2015, 06:41 AM   #5
kmcarr
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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.
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