Hi,
Our lab asked a seq company to do the illumina seq for a snail. However, the illumina reads they produced seem have some problems, since I used jellyfish to do k-mer analysis, and didn't find any coverage peaks even after quality filtration and trimming for 50x coverage - which shows very high quality score in fastqc check. Since the reads have expected hits in our transcriptome, we can rule out reads contamination. Then the only possible reason I could think is the reads quality scale is completely wrong in base calling procedure. For example, it's put Q30 on , but actually it's Q10 or lower.
Could anyone give us some ideas how the base calling procedure would fail in seq process, and could anyone give us some suggestions ? We have already spent huge amount of money on it...
Thank you very much!!
Looking forward to your reply!
Best,
Qing
Our lab asked a seq company to do the illumina seq for a snail. However, the illumina reads they produced seem have some problems, since I used jellyfish to do k-mer analysis, and didn't find any coverage peaks even after quality filtration and trimming for 50x coverage - which shows very high quality score in fastqc check. Since the reads have expected hits in our transcriptome, we can rule out reads contamination. Then the only possible reason I could think is the reads quality scale is completely wrong in base calling procedure. For example, it's put Q30 on , but actually it's Q10 or lower.
Could anyone give us some ideas how the base calling procedure would fail in seq process, and could anyone give us some suggestions ? We have already spent huge amount of money on it...
Thank you very much!!
Looking forward to your reply!
Best,
Qing
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