HTSMultiQC-cleaning-report
A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-08-21, 01:58 UTC
based on data in:
/share/workshop/original_dataset/01-HTS_Preproc
General Statistics
| Sample Name | M Input | M Output |
|---|---|---|
| mouse_110_WT_C | 4.00 | 2.51 |
| mouse_110_WT_NC | 4.00 | 3.02 |
| mouse_148_WT_C | 4.00 | 2.97 |
| mouse_148_WT_NC | 4.00 | 2.81 |
| mouse_158_WT_C | 4.00 | 3.16 |
| mouse_158_WT_NC | 4.00 | 2.88 |
| mouse_183_KOMIR150_C | 4.00 | 2.75 |
| mouse_183_KOMIR150_NC | 4.00 | 2.09 |
| mouse_198_KOMIR150_C | 4.00 | 2.95 |
| mouse_198_KOMIR150_NC | 4.00 | 3.05 |
| mouse_206_KOMIR150_C | 4.00 | 1.59 |
| mouse_206_KOMIR150_NC | 4.00 | 1.19 |
| mouse_2670_KOTet3_C | 4.00 | 3.08 |
| mouse_2670_KOTet3_NC | 4.00 | 3.13 |
| mouse_7530_KOTet3_C | 4.00 | 2.86 |
| mouse_7530_KOTet3_NC | 4.00 | 3.19 |
| mouse_7531_KOTet3_C | 4.00 | 2.99 |
| mouse_7532_WT_NC | 4.00 | 3.05 |
| mouse_H510_WT_C | 4.00 | 2.85 |
| mouse_H510_WT_NC | 4.00 | 3.13 |
| mouse_H514_WT_C | 4.00 | 2.61 |
| mouse_H514_WT_NC | 4.00 | 3.03 |
HTStream
HTStream quality control and processing pipeline for High Throughput Sequencing data.
Processing Overview
Plots reduction of reads and basepairs across the preprocessing pipeline.
hts_Stats_1 Table
Basic statistics about the reads in a dataset.
initial stats
| Sample Name | % R1 Q30 | % R2 Q30 | GC Content | N Content |
|---|---|---|---|---|
| mouse_110_WT_C | 91.17% | 83.09% | 52.89% | 0.0010% |
| mouse_110_WT_NC | 91.52% | 88.46% | 51.46% | 0.0008% |
| mouse_148_WT_C | 92.90% | 87.36% | 51.35% | 0.0007% |
| mouse_148_WT_NC | 90.44% | 86.29% | 52.17% | 0.0011% |
| mouse_158_WT_C | 92.71% | 88.81% | 50.89% | 0.0008% |
| mouse_158_WT_NC | 92.40% | 86.52% | 52.32% | 0.0008% |
| mouse_183_KOMIR150_C | 93.04% | 87.39% | 51.89% | 0.0009% |
| mouse_183_KOMIR150_NC | 91.41% | 82.10% | 54.17% | 0.0009% |
| mouse_198_KOMIR150_C | 93.06% | 88.10% | 51.71% | 0.0011% |
| mouse_198_KOMIR150_NC | 92.51% | 87.89% | 51.53% | 0.0007% |
| mouse_206_KOMIR150_C | 90.55% | 72.27% | 56.32% | 0.0009% |
| mouse_206_KOMIR150_NC | 86.27% | 77.52% | 55.99% | 0.0009% |
| mouse_2670_KOTet3_C | 92.59% | 87.85% | 51.27% | 0.0007% |
| mouse_2670_KOTet3_NC | 92.36% | 88.31% | 51.13% | 0.0007% |
| mouse_7530_KOTet3_C | 92.69% | 86.45% | 51.62% | 0.0009% |
| mouse_7530_KOTet3_NC | 91.72% | 86.42% | 51.11% | 0.0008% |
| mouse_7531_KOTet3_C | 91.15% | 85.94% | 51.24% | 0.0007% |
| mouse_7532_WT_NC | 93.16% | 87.70% | 51.31% | 0.0010% |
| mouse_H510_WT_C | 91.98% | 85.62% | 52.16% | 0.0010% |
| mouse_H510_WT_NC | 91.97% | 88.70% | 50.98% | 0.0011% |
| mouse_H514_WT_C | 91.15% | 83.95% | 52.63% | 0.0009% |
| mouse_H514_WT_NC | 92.61% | 86.31% | 51.25% | 0.0011% |
hts_Stats_1 PE Read Length
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 |
hts_Stats_1 PE Base by Cycle
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.
hts_Stats_1 PE Quality by Cycle
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.
hts_SeqScreener_1
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
screen phix
hts_SeqScreener_2
A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.
count the number of rRNA reads
hts_SuperDeduper
A reference free duplicate read removal tool.
remove PCR duplicates
hts_AdapterTrimmer
Trims adapters which are sequenced when the fragment insert length is shorter than the read length.
trim adapters
hts_PolyATTrim
Attempts to trim poly-A and poly-T sequences from the end of reads.
remove polyAT tails
hts_NTrimmer
Trims reads to the longest subsequence that contains no N's.
remove any remaining N characters
hts_QWindowTrim
Uses a sliding window approach to remove the low quality ends of reads.
quality trim the ends of reads
hts_LengthFilter
Discards reads below a minimum length threshold.
remove reads < 50bp
hts_Stats_2 Table
Basic statistics about the reads in a dataset.
final stats
| Sample Name | % R1 Q30 | % R2 Q30 | GC Content | N Content |
|---|---|---|---|---|
| mouse_110_WT_C | 95.87% | 93.25% | 50.20% | 0.0000% |
| mouse_110_WT_NC | 96.09% | 94.46% | 50.25% | 0.0000% |
| mouse_148_WT_C | 96.03% | 94.02% | 49.92% | 0.0000% |
| mouse_148_WT_NC | 96.04% | 94.09% | 50.16% | 0.0000% |
| mouse_158_WT_C | 95.62% | 93.93% | 49.99% | 0.0000% |
| mouse_158_WT_NC | 95.87% | 93.71% | 50.21% | 0.0000% |
| mouse_183_KOMIR150_C | 96.28% | 94.40% | 50.19% | 0.0000% |
| mouse_183_KOMIR150_NC | 96.02% | 93.46% | 50.41% | 0.0000% |
| mouse_198_KOMIR150_C | 96.20% | 94.54% | 50.23% | 0.0000% |
| mouse_198_KOMIR150_NC | 95.83% | 93.79% | 50.35% | 0.0000% |
| mouse_206_KOMIR150_C | 95.18% | 92.17% | 50.01% | 0.0000% |
| mouse_206_KOMIR150_NC | 95.15% | 92.00% | 50.23% | 0.0000% |
| mouse_2670_KOTet3_C | 95.80% | 93.97% | 50.04% | 0.0000% |
| mouse_2670_KOTet3_NC | 95.72% | 94.01% | 50.02% | 0.0000% |
| mouse_7530_KOTet3_C | 96.08% | 94.09% | 49.87% | 0.0000% |
| mouse_7530_KOTet3_NC | 95.19% | 92.75% | 49.83% | 0.0000% |
| mouse_7531_KOTet3_C | 95.69% | 93.05% | 49.74% | 0.0000% |
| mouse_7532_WT_NC | 96.20% | 94.52% | 49.84% | 0.0000% |
| mouse_H510_WT_C | 95.98% | 93.97% | 49.85% | 0.0000% |
| mouse_H510_WT_NC | 96.03% | 94.71% | 49.76% | 0.0000% |
| mouse_H514_WT_C | 96.12% | 94.20% | 49.83% | 0.0000% |
| mouse_H514_WT_NC | 95.99% | 93.53% | 49.74% | 0.0000% |
hts_Stats_2 PE Read Length
Distribution of read lengths for each sample.
hts_Stats_2 PE Base by Cycle
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.
hts_Stats_2 PE Quality by Cycle
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.
