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Keep quality score when correcting with Canu assembler?
I am using Canu assembler to do a de novo assembly of PacBio data. I noticed that when I corrected my reads it produced a .fasta not a .fastq file, therefore... -
NextSeq500 early results
Hi all,
We replaced our Hiseq1000 with a NextSeq, largely due to the expense of the HS maintenance contract and the long run time. Our... -
Weird results at the 51st nucleotide
Hi all,
We just got some bisulfite sequencing data from a set of patients. After running FastQC on a few samples, we observed an extremely... -
Tophat2 and illumina v1.5
Hey everyone,
I'm relatively new to RNAseq analysis and this site has been really helpful about it.
I've got a very specific question... -
Read quality calculation for a base in CCS
Hi guys,
I was wondering if anyone could tell me how PacBio calculates the quality scores while generating CCS sequences.
... -
Low cluster generation and biphasic reads quality!
Hi all,
I had some issues with my last run and I hope someone can help me to find explanations. We loaded a library of 10 pm from a starting... -
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... -
quality score of 41 from illumina 1.5 pipeline?
Hello,
The samples we sent to BGI were sequenced using illumina 1.5 pipeline so the expect read score should be ASCII 66-104. But among... -
bioinformatics
Hey guys!
I was wondering how should I interpret the quality scores coming from results from 454 GS jr cDNA (not paired end) reads?... -
GATK Base Quality Recalibration
Hi all, I haven't seen anyone else mention this so I was wondering if someone could clear something up for me. The GATK base quality recalibration process... -
Detecting FASTQ Quality Score Format
Hello,
I'm trying to determine whether FASTQ reads quality scores are encoded as phred64 or phred33. The naive method I came up with was... -
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... -
The meaning of B in Illumina 1.5 pipeline data?
Hello all,
I have observed an anomaly in all Illumina 1.5 pipeline data. I use Biopieces (www.biopieces.org) for trimming my data...
