| Run started: | Wed May 26 2021 10:45:18 |
|---|---|
| Run ended: | Wed May 26 2021 10:47:24 |
| Workflow runtime: | 0:02:06.255172 |
| Trim galore | |||
|---|---|---|---|
| Description | Argument | Value | |
| Trimming run on samples? | True | ||
| Quality Encoding | --phred33/--pred64 | phred33 | |
| Adapter | -a/--illumina/--nextera/--small_rna | auto | |
| Minimum read length to retain | --trim | 20 | |
| Trim bases below specified Phred score | --qual | 20 | |
| Stringency | --stringency | 1 | |
| Error Rate | -e | 0.1 | |
| Maximum number of N's to allow | --max_n | 5 | |
| Trim N's from read ends | --trim-n | True | |
| R1 5" bases clipped | --clip_R1 | 0 | |
| R1 3" bases clipped | --three_prime_clip_R1 | 0 | |
| R2 5" bases clipped | --clip_R2 | 0 | |
| R2 3" bases clipped | --three_prime_clip_R2 | 0 | |
| Retain unpaired reads | --retain_unpaired | False | |
| R1 unpaired retention length cutoff | --length_1 | 35 | |
| R2 unpaired retention length cutoff | --length_2 | 35 | |
| Original | Trimmed | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Sample | R1 Reads | R1 Bases | R1 FastQC | R2 Reads | R2 Bases | R2 FastQC | R1 Reads | R1 Bases | R2 Reads | R2 Bases | R1 Trim Galore | R2 Trim Galore | R1 FastQC | R2 FastQC | R1 Proportion trimmed (%) | R2 Proportion trimmed (%) | |
| DRR274673 | 278944 | 37041502 | View Report | 278944 | 37182352 | View Report | 278026 | 36843057 | 278026 | 36899243 | View Report | View Report | View Report | View Report | 0.54 % | 0.76 % | |
| Package | Version | |
|---|---|---|
| FastQC | 0.11.9 | Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc |
| CutAdapt | 3.4 | Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), pp. 10-12, doi:https://doi.org/10.14806/ej.17.1.200 |
| MultiQC | 1.10.1 | Ewels, P. et al. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19) pp. 3047-3048, doi:https://doi.org/10.1093/bioinformatics/btw354 |
| Trim Galore | 0.6.6 | Kreuger, F. (2016). Trim Galore: A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data, https://github.com/FelixKrueger/TrimGalore/ |