11 results in 0.0028 seconds.
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What does PHRED stand for?
I know it seems like a silly question to ask, but Google has no answer for me, nor do the papers published by Phil Green and Brent Ewing themselves. The... -
Identifying heteroduplexes in PacBio CCS reads
Hello,
I'm working with circular consensus reads from a PCR product that may contain heteroduplexes. This is because the PCR was generated...Last edited by verheytb; 04-21-2015, 12:45 PM. -
Local drop in Phred score around SNPs in mpileup -- are these false positives?
Hi all,
I am consistently seeing the following pattern that alerts me to a systematic problem in some step in my sequencing/filtering pipeline.... -
fastq files, lowercase and base score
I am working with a bunch of fastq files from various sources. I do not know anything about the sequencing type. I have found that some have not been... -
Any suggestion for calculating overall Phred scale quality score for a sequence?
Hi all,
I have some consensus nucleotides and ptential variant sites with quality scores (phred scale) generated by mpileup and bcftools. We are...Last edited by sulicon; 07-26-2011, 04:31 PM. -
QC in GATK VCF output
Hello,
I've run GATK to call SNPs and got the corresponding VCF output. Now I'm wondering if there are some pre-established cut-offs for... -
Bowtie Paired-End Processing - E Parameter Ignored
Hi,
I was wondering if anyone else has seen strange behavior with Bowtie's paired-end processing?
I've just started looking... -
Illumina FASTQ Quality Scores - Missing Value
Hi there,
I'm having a look at some FASTQ files generated from the Illumina GA pipeline (I think version 1.3). The data is for a series... -
SNP calling - is there an accepted Phred quality threshold?
I just would like to know if there is an established Phred quality threshold in the literature in order to consider a SNP call reliable.
Provided...Last edited by Francesco Lescai; 04-08-2010, 07:23 AM. -
Bowtie mapping quality in SAM
Hi, how do you interpret the quality of the alignment in SAM files generated by bowtie? I only see values being 0 or 255 (for unmapped and mapped sequences),... -
next_phred & Phaster - call for saving images from GA2
This was a very interesting read, slated for release in 2010, Phil Green presented some benchmark data
http://www.bio-itworld.com/news/10/05/0...
