addReadMetrics.pl
Adds raw read metrics for each fastq.gz file
- CG-Pipeline
Quantifies statistics like average read length. Only measures 1% of the reads and extrapolates for the whole file, and so some inconsistencies might be found such as a single sample of a set that has a minimum read length of 38 when all the others have 35 -- in this case, a minimum read length of 35 might be very rare but present.
Table with columns describing metrics of each reads file. Reads are not interleaved and are quantified independently of either R1 or R2.
- File
- avgReadLength
- totalBases - i.e., total number of nucleotides
- minReadLength
- maxReadLength
- avgQuality
- numReads
- PE? - usually will be
nobecause each split read is analyzed separately - coverage - genome coverage calculated by
totalBasesdivided by expected genome size found intaxonProperties.conf - readScore - TODO
- medianFragmentLength - TODO