Hello,
I'm getting reads from a MiSeq machine and noticing that many have 251bp instead of 250bp, and that the last base has a highly skewed base composition. From what I read of the manual, the sequencer always make read_length + 1 cycles of imaging, but only read_length are analyzed (for phasing etc...). Shouldn't the final fastq have all reads the same size and of only 250bp?? Is it ok to cut out the final base or is it a sign that there's something wrong?
Also, a side note: some reads have less than 250bp, and I assume it is because of adapter trimming. If this is the case, then both read1 and read2 of a pair should be trimmed to the same size, otherwise it shouldn't be trusted, no?
Thanks,
Daniel
I'm getting reads from a MiSeq machine and noticing that many have 251bp instead of 250bp, and that the last base has a highly skewed base composition. From what I read of the manual, the sequencer always make read_length + 1 cycles of imaging, but only read_length are analyzed (for phasing etc...). Shouldn't the final fastq have all reads the same size and of only 250bp?? Is it ok to cut out the final base or is it a sign that there's something wrong?
Also, a side note: some reads have less than 250bp, and I assume it is because of adapter trimming. If this is the case, then both read1 and read2 of a pair should be trimmed to the same size, otherwise it shouldn't be trusted, no?
Thanks,
Daniel
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