HTSMultiQC-cleaning-report
A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-06-19, 12:04 PDT
based on data in:
/share/workshop/mrnaseq_workshop/bnjenner/rnaseq_example/01-HTS_Preproc
HTStream
HTStream quality control and processing pipeline for High Throughput Sequencing data.DOI: .
Processing Overview
Plots reduction of reads and basepairs across the preprocessing pipeline.
Stats
Generates a JSON formatted file containing a set of statistical measures about the input read data.
| Sample Name | % R1 Q30 | % R2 Q30 | GC Content | N Content |
|---|---|---|---|---|
| mouse_110_WT_C | 91.17% | 83.13% | 52.92% | 0.0010% |
| mouse_110_WT_NC | 91.60% | 88.51% | 51.47% | 0.0012% |
| mouse_148_WT_C | 93.02% | 87.44% | 51.34% | 0.0011% |
| mouse_148_WT_NC | 90.50% | 86.38% | 52.19% | 0.0010% |
| mouse_158_WT_C | 92.98% | 89.09% | 50.91% | 0.0008% |
| mouse_158_WT_NC | 92.43% | 86.56% | 52.33% | 0.0009% |
| mouse_183_KOMIR150_C | 93.14% | 87.45% | 51.91% | 0.0009% |
| mouse_183_KOMIR150_NC | 91.48% | 82.11% | 54.19% | 0.0009% |
| mouse_198_KOMIR150_C | 93.11% | 88.20% | 51.73% | 0.0011% |
| mouse_198_KOMIR150_NC | 92.75% | 88.15% | 51.53% | 0.0009% |
| mouse_206_KOMIR150_C | 90.60% | 72.35% | 56.37% | 0.0009% |
| mouse_206_KOMIR150_NC | 86.34% | 77.66% | 56.02% | 0.0008% |
| mouse_2670_KOTet3_C | 92.82% | 88.06% | 51.27% | 0.0007% |
| mouse_2670_KOTet3_NC | 92.57% | 88.49% | 51.13% | 0.0009% |
| mouse_7530_KOTet3_C | 92.75% | 86.49% | 51.62% | 0.0011% |
| mouse_7530_KOTet3_NC | 92.06% | 86.86% | 51.13% | 0.0008% |
| mouse_7531_KOTet3_C | 91.41% | 86.24% | 51.24% | 0.0007% |
| mouse_7532_WT_NC | 93.26% | 87.83% | 51.32% | 0.0009% |
| mouse_H510_WT_C | 92.09% | 85.76% | 52.19% | 0.0008% |
| mouse_H510_WT_NC | 92.06% | 88.84% | 51.00% | 0.0010% |
| mouse_H514_WT_C | 91.22% | 84.00% | 52.66% | 0.0009% |
| mouse_H514_WT_NC | 92.70% | 86.45% | 51.26% | 0.0010% |
Read Lengths: Paired End
Distribution of read lengths for each sample.
| Sample Name | R1 Read Lengths | R2 Read Lengths |
|---|---|---|
| mouse_110_WT_C | 101 | 101 |
| mouse_110_WT_NC | 101 | 101 |
| mouse_148_WT_C | 101 | 101 |
| mouse_148_WT_NC | 101 | 101 |
| mouse_158_WT_C | 101 | 101 |
| mouse_158_WT_NC | 101 | 101 |
| mouse_183_KOMIR150_C | 101 | 101 |
| mouse_183_KOMIR150_NC | 101 | 101 |
| mouse_198_KOMIR150_C | 101 | 101 |
| mouse_198_KOMIR150_NC | 101 | 101 |
| mouse_206_KOMIR150_C | 101 | 101 |
| mouse_206_KOMIR150_NC | 101 | 101 |
| mouse_2670_KOTet3_C | 101 | 101 |
| mouse_2670_KOTet3_NC | 101 | 101 |
| mouse_7530_KOTet3_C | 101 | 101 |
| mouse_7530_KOTet3_NC | 101 | 101 |
| mouse_7531_KOTet3_C | 101 | 101 |
| mouse_7532_WT_NC | 101 | 101 |
| mouse_H510_WT_C | 101 | 101 |
| mouse_H510_WT_NC | 101 | 101 |
| mouse_H514_WT_C | 101 | 101 |
| mouse_H514_WT_NC | 101 | 101 |
Base by Cycle: Paired End
Provides a measure of the uniformity of a distribution. The higher the average deviation from 25% is, the more unequal the base pair composition. N's are excluded from this calculation.
Quality by Cycle: Paired End
Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.
SeqScreener
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
SeqScreener 2
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
SuperDeduper
A reference free duplicate read removal tool.
AdapterTrimmer
Trims adapters which are sequenced when the fragment insert length is shorter than the read length.
PolyATTrim
Attempts to trim poly-A and poly-T sequences from the end of reads.
NTrimmer
Trims reads to the longest subsequence that contains no N's.
QWindowTrim
Uses a sliding window approach to remove the low quality ends of reads.
LengthFilter
Discards reads below a minimum length threshold.
Stats 2
Generates a JSON formatted file containing a set of statistical measures about the input read data.
| Sample Name | % R1 Q30 | % R2 Q30 | GC Content | N Content |
|---|---|---|---|---|
| mouse_110_WT_C | 95.91% | 93.29% | 50.22% | 0.0000% |
| mouse_110_WT_NC | 96.16% | 94.53% | 50.26% | 0.0000% |
| mouse_148_WT_C | 96.11% | 94.12% | 49.93% | 0.0000% |
| mouse_148_WT_NC | 96.10% | 94.15% | 50.17% | 0.0000% |
| mouse_158_WT_C | 95.80% | 94.15% | 50.01% | 0.0000% |
| mouse_158_WT_NC | 95.91% | 93.77% | 50.22% | 0.0000% |
| mouse_183_KOMIR150_C | 96.32% | 94.41% | 50.20% | 0.0000% |
| mouse_183_KOMIR150_NC | 96.03% | 93.43% | 50.41% | 0.0000% |
| mouse_198_KOMIR150_C | 96.25% | 94.62% | 50.25% | 0.0000% |
| mouse_198_KOMIR150_NC | 95.97% | 93.96% | 50.36% | 0.0000% |
| mouse_206_KOMIR150_C | 95.23% | 92.27% | 50.02% | 0.0000% |
| mouse_206_KOMIR150_NC | 95.13% | 91.85% | 50.23% | 0.0000% |
| mouse_2670_KOTet3_C | 95.95% | 94.13% | 50.05% | 0.0000% |
| mouse_2670_KOTet3_NC | 95.85% | 94.15% | 50.02% | 0.0000% |
| mouse_7530_KOTet3_C | 96.13% | 94.16% | 49.88% | 0.0000% |
| mouse_7530_KOTet3_NC | 95.44% | 93.09% | 49.84% | 0.0000% |
| mouse_7531_KOTet3_C | 95.87% | 93.26% | 49.75% | 0.0000% |
| mouse_7532_WT_NC | 96.27% | 94.62% | 49.85% | 0.0000% |
| mouse_H510_WT_C | 96.05% | 94.07% | 49.86% | 0.0000% |
| mouse_H510_WT_NC | 96.10% | 94.80% | 49.78% | 0.0000% |
| mouse_H514_WT_C | 96.18% | 94.27% | 49.83% | 0.0000% |
| mouse_H514_WT_NC | 96.06% | 93.63% | 49.75% | 0.0000% |
Read Lengths: Paired End
Distribution of read lengths for each sample.
Base by Cycle: Paired End
Provides a measure of the uniformity of a distribution. The higher the average deviation from 25% is, the more unequal the base pair composition. N's are excluded from this calculation.
Quality by Cycle: Paired End
Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.
