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Hello all,
when comparing the fastq files obtained from illumina/solexa sequencing, we see a huge drop in values. Normally, you would only see a small dip near the 3 prime end, while our current sequences show a dramatic drop when going to the 3 prime end and even their 5 prime end doesn't start at value ~40 (see att).
After contacting people at illumina, they claim that the quality of the reads is still good, but that due to their new pipeline, you can have a drop in the fastq values.
Some questions/remarks.
- Did other people already experience this drop in fastq value?
- How can we now standardize the quality of the reads when these values change over time?
- What about assembly tools that try to incorporate these values in order to perform a better assembly?
- How do you use/interpret these fastQ files?
- Should we recalculate these values as described in following paper: http://www.ncbi.nlm.nih.gov/pubmed/1...ubmed_RVDocSum
Many thanks
Steven
when comparing the fastq files obtained from illumina/solexa sequencing, we see a huge drop in values. Normally, you would only see a small dip near the 3 prime end, while our current sequences show a dramatic drop when going to the 3 prime end and even their 5 prime end doesn't start at value ~40 (see att).
After contacting people at illumina, they claim that the quality of the reads is still good, but that due to their new pipeline, you can have a drop in the fastq values.
Some questions/remarks.
- Did other people already experience this drop in fastq value?
- How can we now standardize the quality of the reads when these values change over time?
- What about assembly tools that try to incorporate these values in order to perform a better assembly?
- How do you use/interpret these fastQ files?
- Should we recalculate these values as described in following paper: http://www.ncbi.nlm.nih.gov/pubmed/1...ubmed_RVDocSum
Many thanks
Steven
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