Hello,
I need to filter my SAM/BAM files to remove bases below a certain base quality (QUAL) threshold, eg. Q30. Does anybody know if there...
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Filtering SAM files by base quality (QUAL)?
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GATK QUAL score not phred scaled
Hi,
I have a specific question about the QUAL score calculated by GATK used by the MiSeq Reporter. The QUAL used to be a phred scaled score,... -
qual format determination
I typically map fastq files taken from the short read archive using bowtie on Galaxy. I'm now moving to the command line. For this, I'll need to know... -
Bowtie2 Bug: error reporting multiple alignments
Hi,
I think I've found a problem with reporting multiple alignments in Bowtie2, and was wondering if anyone else can confirm.
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hello and first questions!
Hello there!
I'm starting with my brand new data from Roche's 454 pyrosequencing and I have some questions at this point.
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Script for converting fastq back to color csfasta and qual
Hello, does anyone know a script to convert a fastq file back to color csfasta and qual? The fastq file is in color (numbers, not double decoded) so I... -
SHRiMP and SOLiD Qualities
I want to run SHRiMP on SOLiD data, but despite reading the manual I can't find a parameter that allows me to give the .qual file as input. Does SHRiMP... -
fasta+qual = sff??
Dear Bioinformatists,
The data I have received has 454 pyrosequence reads in Fasta format and respective quality scores as a .qual file....
