Thanks for the update.
What i´m trying to achieve here is ( so I might be wrong the way i do it) is to compute the quantile at each cycle across all reads. This is working pretty wall with bacterial genomes using 16s amplicons . Now working with higher datasets (metagenomics samples doing shotgun sequencing i get much more data)
So for read1 i will have the score for each cycle (i.g 1..100)
for read i will also get the score for each cycle (again 1..100)
at the end i want a matrix (basically what the as(quality(fq),"matrix") would return. With this matrix i compute the quantile per cycle and generate a boxplot that show the quality per cycle.
See attached plot. Obviously i could just use fastQC from Babraham bioinformatics but that would not be that funny
crashes in my case are problems allocating memory. SInce i don´t need the sequences but just the scores i thought i could just get the quality scores.
modified 2.5 years ago
2.5 years ago by
danova_fr • 20