Closed donkirkby closed 9 years ago
This happened to all the forward reads in the 23 Mar 2015 run. Should we have some limit on how much data we report in the failed_read.csv
file? A typical FASTQ file on this run was about 50MB, so the collated failed_read.csv
file would be roughly 500MB.
Would it be helpful to extend the collated_counts.csv
file through more steps? That way you could see where reads got lost along the way. We'd probably want to consistently report read pairs. Some ideas for entries in the list:
If a read is rejected for low quality in the remap stage, its paired read never gets matched in the sam2aln stage. Currently, that is not reported, but unmatched reads could easily be added to the
failed_read.csv
file.One example is sample 60780A-HLA-B_S72 from the 1 Apr 2015 run.