A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2017-11-18, 23:11 based on data in:
/woldlab/castor/home/dangeles/projects/med_cafe
General Statistics
Showing 66/66 rows and 5/7 columns.| Sample Name | % Aligned | M Aligned | % Dups | % GC | M Seqs |
|---|---|---|---|---|---|
| 18841_AGTCAA_L001_R1_001 | 55.3% | 47% | 10.5 | ||
| 18841_AGTCAA_L002_R1_001 | 55.9% | 47% | 10.8 | ||
| 18842_AGTTCC_L001_R1_001 | 56.4% | 47% | 10.9 | ||
| 18842_AGTTCC_L002_R1_001 | 56.7% | 47% | 11.1 | ||
| 18843_ATGTCA_L001_R1_001 | 55.8% | 47% | 10.2 | ||
| 18843_ATGTCA_L002_R1_001 | 56.4% | 47% | 10.5 | ||
| 18844_CCGTCC_L001_R1_001 | 51.7% | 46% | 10.8 | ||
| 18844_CCGTCC_L002_R1_001 | 52.5% | 46% | 11.1 | ||
| 18845_GTCCGC_L001_R1_001 | 50.8% | 47% | 9.4 | ||
| 18845_GTCCGC_L002_R1_001 | 51.3% | 47% | 9.6 | ||
| 18846_GTGAAA_L001_R1_001 | 51.1% | 46% | 9.6 | ||
| 18846_GTGAAA_L002_R1_001 | 51.4% | 46% | 9.8 | ||
| 18847_GTGGCC_L001_R1_001 | 54.4% | 47% | 10.3 | ||
| 18847_GTGGCC_L002_R1_001 | 55.0% | 47% | 10.5 | ||
| 18848_GTTTCG_L001_R1_001 | 55.6% | 47% | 10.5 | ||
| 18848_GTTTCG_L002_R1_001 | 56.3% | 47% | 10.7 | ||
| 18849_CGTACG_L001_R1_001 | 54.3% | 46% | 9.9 | ||
| 18849_CGTACG_L002_R1_001 | 55.0% | 46% | 10.2 | ||
| 18850_GAGTGG_L001_R1_001 | 57.4% | 47% | 12.8 | ||
| 18850_GAGTGG_L002_R1_001 | 57.7% | 47% | 13.1 | ||
| 18851_ACTGAT_L001_R1_001 | 55.8% | 47% | 12.0 | ||
| 18851_ACTGAT_L002_R1_001 | 56.3% | 47% | 12.3 | ||
| 18852_ATTCCT_L001_R1_001 | 58.3% | 47% | 13.6 | ||
| 18852_ATTCCT_L002_R1_001 | 58.7% | 46% | 14.0 | ||
| 18853_ATCACG_L001_R1_001 | 55.6% | 47% | 12.5 | ||
| 18853_ATCACG_L002_R1_001 | 55.8% | 47% | 12.8 | ||
| 18854_CGATGT_L001_R1_001 | 53.1% | 46% | 12.4 | ||
| 18854_CGATGT_L002_R1_001 | 53.7% | 46% | 12.7 | ||
| 18855_TTAGGC_L001_R1_001 | 56.3% | 47% | 12.9 | ||
| 18855_TTAGGC_L002_R1_001 | 57.2% | 47% | 13.2 | ||
| 18889_AGTCAA_L001_R1_001 | 54.0% | 47% | 10.3 | ||
| 18889_AGTCAA_L002_R1_001 | 53.4% | 47% | 10.2 | ||
| 18890_AGTTCC_L001_R1_001 | 53.8% | 47% | 10.0 | ||
| 18890_AGTTCC_L002_R1_001 | 53.7% | 47% | 9.9 | ||
| 18891_ATGTCA_L001_R1_001 | 56.7% | 47% | 10.9 | ||
| 18891_ATGTCA_L002_R1_001 | 56.6% | 47% | 10.8 | ||
| 18892_CCGTCC_L001_R1_001 | 56.3% | 47% | 11.4 | ||
| 18892_CCGTCC_L002_R1_001 | 55.8% | 47% | 11.3 | ||
| 18893_GTCCGC_L001_R1_001 | 56.3% | 47% | 11.0 | ||
| 18893_GTCCGC_L002_R1_001 | 56.4% | 47% | 11.0 | ||
| 18894_GTGAAA_L001_R1_001 | 55.7% | 47% | 11.0 | ||
| 18894_GTGAAA_L002_R1_001 | 55.6% | 47% | 10.9 | ||
| 18895_GTGGCC_L001_R1_001 | 57.9% | 47% | 13.0 | ||
| 18895_GTGGCC_L002_R1_001 | 57.9% | 47% | 12.9 | ||
| Project_18841_index13 | 94.9% | 21.6 | |||
| Project_18842_index14 | 94.4% | 22.3 | |||
| Project_18843_index15 | 94.2% | 21.0 | |||
| Project_18844_index16 | 94.1% | 22.1 | |||
| Project_18845_index18 | 93.5% | 19.0 | |||
| Project_18846_index19 | 94.3% | 19.6 | |||
| Project_18847_index20 | 94.0% | 21.0 | |||
| Project_18848_index21 | 92.5% | 21.0 | |||
| Project_18849_index22 | 94.5% | 20.4 | |||
| Project_18850_index23 | 94.9% | 26.2 | |||
| Project_18851_index25 | 94.6% | 24.6 | |||
| Project_18852_index27 | 94.4% | 27.9 | |||
| Project_18853_index1 | 94.5% | 25.7 | |||
| Project_18854_index2 | 91.3% | 24.5 | |||
| Project_18855_index3 | 94.1% | 26.5 | |||
| Project_18889_index13 | 93.1% | 20.6 | |||
| Project_18890_index14 | 93.4% | 19.9 | |||
| Project_18891_index15 | 94.0% | 22.0 | |||
| Project_18892_index16 | 93.6% | 22.9 | |||
| Project_18893_index18 | 94.5% | 22.4 | |||
| Project_18894_index19 | 94.5% | 22.3 | |||
| Project_18895_index20 | 94.0% | 26.2 |
RSeQC
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.
Read Distribution
Read Distribution calculates how mapped reads are distributed over genome features.
Gene Body Coverage
Gene Body Coverage calculates read coverage over gene bodies. This is used to check if reads coverage is uniform and if there is any 5' or 3' bias.
FastQC
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
Sequence Quality Histograms
The mean quality value across each base position in the read. See the FastQC help.
Per Sequence Quality Scores
The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
Per Base Sequence Content
The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
Click a heatmap row to see a line plot for that dataset.
rollover for sample name
Per Sequence GC Content
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.
Per Base N Content
The percentage of base calls at each position for which an N was called. See the FastQC help.
Sequence Length Distribution
All samples have sequences of a single length (50bp).
Sequence Duplication Levels
The relative level of duplication found for every sequence. See the FastQC help.
Overrepresented sequences
The total amount of overrepresented sequences found in each library. See the FastQC help for further information.
Adapter Content
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
