A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2018-04-06, 16:47 based on data in:
/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_WDir
General Statistics
Showing 15/15 rows and 14/15 columns.| Sample Name | % Aligned | M Pairs | % Used pairs | % Mapped | Min RE dist | Max RE dist | Frag Length | M Aligned | % Aligned | M Aligned | % Aligned | % Aligned | M Aligned | % Trimmed |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 | 5.9% | |||||||||||||
| HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 | 83.7% | 167.9bp | 48.5 | |||||||||||
| HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 | 31.0% | |||||||||||||
| HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 | 7.7% | |||||||||||||
| HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 | 84.5% | 169.4bp | 59.3 | |||||||||||
| HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 | 32.2% | |||||||||||||
| bismark_SE_report | 69.7% | |||||||||||||
| bowtie2_1 | 98.3% | |||||||||||||
| bowtie2_2 | 98.3% | |||||||||||||
| hicexplorer_hicexplorer1_small_test | 0.1 | 37.3% | 91.2% | 303 bp | 800 bp | |||||||||
| hicexplorer_hicexplorer2_small_test_rf | 0.1 | 35.9% | 91.2% | 152 bp | 1500 bp | |||||||||
| hisat2_1 | 96.2% | |||||||||||||
| hisat2_2 | 96.2% | |||||||||||||
| star_log | 89.0% | 0.0 | ||||||||||||
| tophat_align | 99.5% | 0.3 |
Bismark
Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.
Alignment Rates
Strand Alignment
HiCExplorer
HiCExplorer addresses the common tasks of Hi-C analysis from processing to visualization.
Mapping statistics
This shows how the sequenced read pairs were mapped and those filtered due to mapping problems.
- Pairs mappable, unique and high quality
- The count of reads that were considered as valid reads and were not one of the following:
- One mate unmapped
- Filtered out read because one mate was not mapped.
- One mate not unique
- Filtered out read because one mate was not unique.
- One mate low quality
- Filtered out because one mate was having a low quality.
Read filtering
This figure contains the number of reads that were finally used to build the Hi-C matrix along with the reads that where filtered out.
- Dangling ends
- These are reads that start with the restriction site and constitute reads that were digested but no ligated.
- Same fragment
- These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in between.
- These read pairs are not valid Hi-C pairs.
- Self circle
- Self circles are defined as pairs within 25kb with 'outward' read orientation
- Self ligation
- These are read pairs with a restriction site in between that are within 800 bp.
Contact distance
This figure contains information about the distance and location of the valid pairs used.
- Long range
- Pairs with a distance greater than 20 kilobases
- Short range
- Pairs with a distance less than 20 kilobases
- Inter chromosomal
- Interchromosomal pairs.
Read orientation
This figure contains information about the orientation of the read pairs.
- Inward pairs
- First mate is a forward read, second is reverse.
---------------> <----------------
- Outward pairs
- First mate is a reverse read, second is forward.
---------------> <----------------
- Left pairs
- Both are reverse reads.
<--------------- <----------------
- Right pairs
- Both are forward reads.
---------------> ---------------->
STAR
STAR is an ultrafast universal RNA-seq aligner.
Alignment Scores
Gene Counts
Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.
HISAT2
HISAT2 is a fast and sensitive alignment program for mapping NGS reads (both DNA and RNA) against a reference genome or population of reference genomes.
Tophat
Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes.
Bowtie 2
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
This plot shows the number of reads aligning to the reference in different ways.
There are 3 possible types of alignment: SE Mapped uniquely: Read has only one occurence in the reference genome. SE Multimapped: Read has multiple occurence. * SE No aligned: Read has no occurence.
Cutadapt
Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.
This plot shows the number of reads with certain lengths of adapter trimmed. Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length. See the cutadapt documentation for more information on how these numbers are generated.
