A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2021-03-03, 13:42
based on data in:
/home/cri.camres.org/sawle01/Documents/training/Bulk_RNAseq_Course_2021/Course_Materials/metrics
General Statistics
Showing 13/13 rows and 5/6 columns.| Sample Name | % rRNA | % mRNA | % Aligned | Insert Size | % Dups |
|---|---|---|---|---|---|
| SRR7657872 | % | 88.2% | 93% | 253 bp | 22.1% |
| SRR7657873 | % | 89.8% | 93% | 259 bp | 24.9% |
| SRR7657874 | % | 88.5% | 83% | 264 bp | 21.8% |
| SRR7657875 | % | 94.1% | 94% | 259 bp | 24.9% |
| SRR7657876 | % | 92.1% | 94% | 258 bp | 25.5% |
| SRR7657877 | % | 89.2% | 94% | 256 bp | 24.3% |
| SRR7657878 | % | 91.7% | 94% | 263 bp | 25.1% |
| SRR7657879 | % | 89.9% | 94% | 251 bp | 24.5% |
| SRR7657880 | % | 89.0% | 94% | 261 bp | 22.6% |
| SRR7657881 | % | 88.5% | 94% | 262 bp | 24.2% |
| SRR7657882 | % | 89.4% | 94% | 261 bp | 29.0% |
| SRR7657883 | % | 91.6% | 95% | 259 bp | 24.1% |
| SRR7657893 | % | 88.6% | 43% | 195 bp | 23.5% |
Picard
Picard is a set of Java command line tools for manipulating high-throughput sequencing data.
Alignment Summary
Please note that Picard's read counts are divided by two for paired-end data.
Insert Size
Plot shows the number of reads at a given insert size. Reads with different orientations are summed.
Mark Duplicates
Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.
The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.
To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:
READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATESREADS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATESREADS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATESREADS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICALREADS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATESREADS_UNMAPPED = UNMAPPED_READS
RnaSeqMetrics Assignment
Number of bases in primary alignments that align to regions in the reference genome.
RIBOSOMAL_INTERVALS parameter, as documented here.
