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• Ngs Dna Read Simulator With Quality Scores Available?
  Hi all, I am looking to generate some simulated Illumina 100bp paired end DNA reads. I have tr...
• Read To Consensus Quality Scores
  Hi, what is the actual formula for finding the quality score in a consensus sequence base? I'l...
• 'Perfect' RNA-seq base quality score
  Hi everyone, I am new to RNA-seq and have I recently performed RNA-seq (Illumina NovaSeq 6000; 2...
• Quality filtering of reads with more than K bases under quality score
  Hey all, I am currently working on an analysis of barcode sequencing and looking for a tool to f...
• Quality trimming for denovo assembly
  Is quality trimming of raw reads (Illumina Paired End; 2 X 300 bp) for de novo assembly using SPA...
• Comparing Quality Of Read 1 And Read2 Of Illumina Pe
  Hello: I have been asked to compare the quality of read one and read 2 of a illumina PE sequencin...
• Need an advice on quality control of illumina reads
  Hi, I have a dataset generated by illumina MiSeq. FastQC failed the per base sequence quality an...
• How To Select The Top 30% Variants (Based On Quality) From A Vcf File?
  How can I select the top 30% variants (based on quality) from a VCF file? So all the the varia...
• samtools mpileup on mitochondrial bam results in incorrect base quality scores
  I am trying to do some analysis on the mitochondrial genome, specifically examining variants. The...
• NovaSeq quality analysis
  Hi all, I tested NovaSeq data. It can actually be very accurate! In my tests, R1 had an 86% ra...
• Blastn on illumina reads for contamination detection before or after quality filtering?
  Should you blastn illumina reads for contamination before or after you have quality controlled t...
• trimming nano pore reads based on quality score.
  Hello all, I am trying to trim the nanopore sequences based on the quality of the reads. The Oxf...
• Mapping quality score of clipped reads
  Hi, I have a question please. For soft-clipped or hard-clipped reads, for example a read with a c...
• Filter reads by calculating the distribution of phred score in each individual read
  Dear All, I would like to know if there is any tool or script to calculate the distribution of PH...
• Is MAPQ score related to Phred quality score?
  Hi, I just wanted to know although the two quality scores have different formulae to calculate th...
• samtools Mpileup quality scores?
  Dear all, What is the default quality scores expected by samtools mpileup? I see you can specif...
• Cap3 Assembly
  Does CAP3 always allocate a Q20 score to all the bases in the final assembled contig when assembl...
• Converting Illumina fastq quality scores to phred
  I have been trying to understand how to calculate probabilities of correct calls in my Illumina d...
• Should I use reads with good quality but failed-vendor flag?
  Hi guys, Quick question is: I have some mapped reads in bam file which have good read quality, b...
• Strange Alignment Issue
  I have encountered a strange issue in the alignment of a whole genome from Illumina. The below im...