Hello,
I'm very new to analysing next gen data, and I was hoping someone might be able to help me interpret a failed diagnostic plot I've just obtained in FastQC.
I was wondering if anyone had come across anything similar to the per base score quality read I just got in FastQC (see attached picture)? It doesn't look anything like the other 'failed' example plots, and I'm at a bit of a loss as to why base 11 in particular is so poor... is this indicative of contamination/sequencing reaction failure/short sequences?
Secondly, is it actually possible to assemble such 'failed' data? And is there anything I should specifically be doing in terms of assembly/quality filtering/trimming? I'd be very grateful of any suggestions!
This is single end, ancient DNA sequence data, and this is the plot for all the sequences with the correct tag sequence.
Many thanks for your help.
I'm very new to analysing next gen data, and I was hoping someone might be able to help me interpret a failed diagnostic plot I've just obtained in FastQC.
I was wondering if anyone had come across anything similar to the per base score quality read I just got in FastQC (see attached picture)? It doesn't look anything like the other 'failed' example plots, and I'm at a bit of a loss as to why base 11 in particular is so poor... is this indicative of contamination/sequencing reaction failure/short sequences?
Secondly, is it actually possible to assemble such 'failed' data? And is there anything I should specifically be doing in terms of assembly/quality filtering/trimming? I'd be very grateful of any suggestions!
This is single end, ancient DNA sequence data, and this is the plot for all the sequences with the correct tag sequence.
Many thanks for your help.
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