Is this common? Or there are ways around getting high error rates after cycle 50 for long reads? Especially read2 looks pretty bad!
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I need a little more info on this. What are you aligning to? What chemistry are you using? Is this PhiX? If you're using the v2 kits and this is PhiX than yes these are very high, it should be below 5% at cycle 75 for both reads on a decent run.
The reason for this could range from degraded reagents, to out of focus images to a bad turn around on the PE module, etc. etc.
Brad
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Well first off you might want to use the human cDNA library as a reference genome. The human genomic reference isn't going to work with ELAND very well. Eland doesn't support gaps (read introns). This still doesn't explain the higher error rates on the paired end read, that's probably a chemistry or technician issue.
Brad
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This is typically what I see regardless of the run length we do, ie, similar curves to what you posted for our 60 x 60 and 85 x 85 runs. I don't think it's a technician issue. Because the curve does look proportionally similar (ie, starts to rise at about the same percentage into the read, not at a particular base) I think it may be a phasing or base calling issue. I'm also suspecting reagent longevity--our next long run will use freshly made topped off reagents like the old days just to see if that helps.
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Originally posted by basickler View PostWell first off you might want to use the human cDNA library as a reference genome. The human genomic reference isn't going to work with ELAND very well. Eland doesn't support gaps (read introns). This still doesn't explain the higher error rates on the paired end read, that's probably a chemistry or technician issue.
Brad--
bioinfosm
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Originally posted by bioinfosm View PostIs this common? Or there are ways around getting high error rates after cycle 50 for long reads? Especially read2 looks pretty bad!
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Originally posted by bioinfosm View PostIs this common? Or there are ways around getting high error rates after cycle 50 for long reads? Especially read2 looks pretty bad!
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