Thornton_080620
- Project Type
- RNA-seq
- Library Preparation
- TruSeq Stranded mRNA
- Sequencing Platform
- Illumina NextSeq550
- Data Formatting
- bcltofastq-2.19.0
- Data Cleaning
- fastp 0.20.0, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
- Genome Alignment
- STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
- Reference Genome
- GRCm38.p6 + Gencode-M22 Annotation
- Read Quantification1
- subread-1.6.4, featurecounts, -s 2 -t exon -g gene_name
- Read Quantification3
- salmon-0.13.1, --seqBias --gcBias --posBias
Report generated on 2020-08-25, 11:27 based on data in:
/gpfs/fs2/scratch/grc_group/current_projects/Project_Thornton_080620
General Statistics
Showing 8/8 rows and 10/12 columns.| Sample Name | % Duplication | GC content | % PF | % Adapter | % Aligned | M Aligned | % Assigned | M Assigned | % Aligned | M Aligned |
|---|---|---|---|---|---|---|---|---|---|---|
| Heart1 | 50.5% | 44.9% | 95.0% | 3.1% | 67.1% | 28.2 | 44.9% | 25.9 | 93.2% | 39.2 |
| Heart2 | 52.1% | 45.6% | 95.4% | 2.9% | 68.8% | 30.2 | 46.8% | 27.9 | 93.7% | 41.2 |
| Heart3 | 51.1% | 45.9% | 95.3% | 2.9% | 70.5% | 27.6 | 48.9% | 25.4 | 92.7% | 36.3 |
| Heart4 | 53.4% | 44.7% | 95.3% | 3.1% | 66.0% | 26.8 | 44.3% | 24.8 | 93.9% | 38.1 |
| Heart5 | 53.4% | 44.5% | 95.4% | 3.2% | 63.8% | 26.7 | 41.7% | 24.6 | 93.5% | 39.2 |
| Heart6 | 55.6% | 45.0% | 95.4% | 3.1% | 66.1% | 26.5 | 44.2% | 24.6 | 93.8% | 37.6 |
| Heart7 | 50.1% | 45.0% | 95.2% | 3.1% | 68.0% | 22.7 | 45.6% | 20.7 | 93.0% | 31.0 |
| Heart8 | 49.1% | 44.9% | 94.8% | 3.2% | 67.5% | 22.3 | 45.2% | 20.4 | 93.2% | 30.8 |
FastP
FastP An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)
Filtered Reads
Filtering statistics of sampled reads.
Duplication Rates
Duplication rates of sampled reads.
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Sequence Quality
Average sequencing quality over each base of all reads.
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GC Content
Average GC content over each base of all reads.
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N content
Average N content over each base of all reads.
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FeatureCounts (Unique Reads)
Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
