NHD13_GEO
- Project Type
- RNA-seq
- Library Preparation
- Standard Illumina Total RNA Stranded
- Sequencing Platform
- Illumina HiSeq 2000
- Data Formatting
- bcltofastq-2.19.1
- Data Cleaning
- fastp 0.23.1, --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_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
- Reference Genome
- GRCm39 + M31
- Read Quantification1
- subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
- Read Quantification3
- salmon-1.5.2, --seqBias --gcBias --posBias
Report
generated on 2023-07-06, 07:41
based on data in:
/gpfs/fs2/scratch/grc_group/tyler_ongoing/for_development/Project_NHD13_GEO
General Statistics
Showing 6/6 rows and 10/12 columns.| Sample Name | % Duplication | GC content | % PF | % Adapter | % Aligned | M Aligned | % Assigned | M Assigned | % Aligned | M Aligned |
|---|---|---|---|---|---|---|---|---|---|---|
| NHD13_1 | 41.3% | 49.1% | 96.3% | 80.6% | 13.5 | 50.1% | 11.5 | 88.8% | 14.9 | |
| NHD13_2 | 41.1% | 48.8% | 96.4% | 81.4% | 14.1 | 52.4% | 12.3 | 91.5% | 15.9 | |
| NHD13_3 | 40.9% | 48.7% | 96.5% | 0.8% | 81.4% | 14.2 | 52.0% | 12.3 | 90.9% | 15.9 |
| WT_1 | 40.0% | 48.4% | 96.5% | 81.8% | 12.5 | 52.7% | 10.8 | 90.9% | 13.9 | |
| WT_2 | 40.5% | 48.8% | 96.4% | 0.8% | 82.2% | 13.4 | 53.5% | 11.7 | 91.3% | 14.9 |
| WT_3 | 42.0% | 48.2% | 96.4% | 0.6% | 81.8% | 14.2 | 52.7% | 12.3 | 91.2% | 15.8 |
FastP
FastP An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)
Filtered Reads
Filtering statistics of sampled reads.
Sequence Quality
Average sequencing quality over each base of all reads.
loading..
GC Content
Average GC content over each base of all reads.
loading..
N content
Average N content over each base of all reads.
loading..
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.
