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I have found in our metagenomics analys (Illumina 2x150 bp) number of reads that contain only single nucleotide (G). The proportion of these reads is not high, about 0.004 % in forward reads and 0.16 % in reverse reads, but still is this normal sequencing error? Should I discard these reads or ignore them? I think they might mess up contigs assembly.
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Is this a NextSeq 500 run? A G call is the absence of signal at a cluster in NextSeqs, and polyG reads were seen, particularly with the v1 reagents.Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com -
Yes, it's a NextSeq 500 run, but v2 reagents. But when they are empty signal clusters then I'll just remove them.Comment
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