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• Per base sequence quality and per base N content
  Hi, I have one incomprehensibleness with my FastQC's report. Usually N's have quality=2, so if o...
• High A in "Per base sequence content" of fastQC report
  In my RNA sequencing fastqc report, I consistently notice an abnormally high A (green) peak in se...
• Why does the per base sequence quality decrease over the read in Illumina?
  **Why does the per base sequence quality decrease over the read in Illumina?** The first indicat...
• Should I remove Kmers identified in FastQC?
  Hi, apologies for this basic questions, I new in NGS quality control. I have been check my NGS da...
• Sequence Length Distribution after trimmomatic
  Hello, I have trimmed my sequences with TRIMMOMATIC using the following command: trimmomati...
• What could be the best explanation for a dip in phred quality score at the near beginning of reads?
  I am looking at reverse read (R2) from a dataset from 2X150 paired end Illumina platform, transcr...
• Decreased base quality at start of RNA seq reads
  Hey all, While running quality control steps for an RNA-Seq experiment I can see a decrease in t...
• How would you trim this RNA-seq data
  Hi, I am working on an RNA-Seq project. We just got back some sequencing and I had a couple que...
• Bimodal %GC plot of fastqc output in RNASeq
  Dear all, Recently I performed RNASeq 150 bp paired-ends reads in rice (Illumina). I performed fa...
• How to interpret Per sequence GC content module in FastQC for RNA-seq data?
  The Per sequence GC content graph gives an idea of contamination in present. How do we identify t...
• How to interpret fast or multiQC reports of easy HiC or HiC data
  Hello, I have got fastqs from an easy-HiC sequencing experiment: the samples are embrionic stem c...
• Having multiple adapter sequence in raw fastq files?
  Dear all, I have 50 RNA-Seq samples for a project. FastQC reports different **TruSeq Adapter, In...
• Per base sequence content
  Good afternoon! I'd like some help in a problem I have been facing in trimming my sequenced geno...
• fastqc report of miseq data
  Hi everyone, I recently got into analyzing 16S rRNA data (miseq). I performed quality check with...
• Fastq file with very high per base sequence quality and no box-whisker plot
  Hello, I am currently working with Fastq files of illumina sequencing with a coverage of 150x (p...
• The quality of intermediate base of read is not good.
  Hi I have some RANseq data. When I use fastQC to do quality control,The results are as follows: !...
• How to analyze the RNAseq paired samples with DESeq2?
  I am a graduate student who works with the RNAseq data for the first time. I have been stuck on D...
• FastQC report explanation on example
  Hi there! I have tried to make some quality control of NGS fastq files in FastQC. I've read the ...
• A peak on FastQC graph Sequence Duplication Levels on MNase seq data
  Good time to anyone! Here I have the result of MNase seq data analysis using FastQC. The problem ...
• fastqc quality leading reads are all same
  I get 16sRNA sequencing from illumina MiSeq. I Run fastQC and I get the following quality plot. ...
• single end reads, reverse and forward primer
  I have forward and reverse single end reads. I can distinguish them from fastq file according to...
• Trimming RNA-Seq Data
  Hi, I had a couple questions about some RNA-Seq data. A colleague recently received some RNA-Seq...
• Is it normal to obtain a perfectly dark blue "Per tile sequence quality" plot in fastqc?
  Hello. I ran fastqc quality check on WES paired end reads. I got very high Per base sequence qua...
• I got extremely low alignment rate running HiSAT2 and Tophat2
  Hi. I'm trying to map paired-end rna-seq reads on GRCm38 (mm10) using Hisat2 and Tophat2. But the...