Hi all,
i am wondering what are possible causes of low Q30 scores, apart from overclustering?
I am working with amplicon...
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quality score issues
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sequence and quality are inconsistent - modifying sam files to reflect differe ASCII
I ran into the "sequence and quality are inconsistent" error when trying to use samtools view -Sb on some bwa aln sam files. I read in a previous... -
Calculating consensus quality scores
Hi All,
I am new to this forum and looking for advice on what the proper way is to calculate a consensus quality scores for paired end reads.... -
PacBio RS quality score output definition (FASTQ)
I'm simulating reads that mimic PacBio's data (long reads, about 1k-20k bases). Other things are pretty well in order, but I'd like to know what kind... -
MiSeq fastQ quality scores
I have fastQ files as output from MiSeq, 300bp directional reads. I would like to plot the distribution of quality scores for all bases (using Perl, Gnuplot... -
Fastx giving error for Illumina data
Hi,
I'm trying to do some quality scoring/trimming on some Illumina, SE RNAseq data, but keep getting an unusual error message from Fastx.... -
mpileup base-quality filter does not seem to work
Hello,
I am trying to detect somatic mutations on tumor-normal samples (illumina paired-end reads), so what I am doing as the first approach... -
Which format of reads quality is assumed in bfast bwaaln command
Hello,
I am using bfast to align reads (paired-end) from Illumina GAIIx, so the first step is to perform the bfast bwaaln command. I am... -
samtools SNP Quality Scores in Depth
Hi All,
I am been analyzing the quality score distribution reported by samtools for both variant and reference sites (QUAL) in exome and... -
BWA mapping fastq files with Illumina quality
Hello,
I am still new in these matters, I was told to map illumina reads to the human genome. I was given the fastq files and proceeded...
