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Eigen_phred_coding values interpretation
written by Lukas •I have problem with understanding how to interpret Eigen_phred score. I understand the main goal of this tool and know that score value would look …
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How is the ABQ field in the VCF file calculated?
written by brunomoda •The only information I found about this field was in the header: ``` ABQ = Average quality of variant-supporting bases (qual2) ```` Can someone provide …
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messed up SRA quality scores
written by Noah •I'm having an issue with sequences I download from the SRA having apparently incorrect base quality scores. I downloaded the NCBI SRA run SRR4181534 using …
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working with .sra-lite files
written by RaygozakHi, i'm seeing more and more this .sra-lite files which supposedly have a simplified base score. However, I only see reads with all qualities set …
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FASTQ Phred33 average base quality score
written by oarsI have a FASTQ dataset where I'm trying to find the average base quality score. I found this old link that helped somewhat (https://www.biostars.org/p/47751/). Here …
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Bismark: Minimum MAPQ threshold (MMT) and Minimum Phred threshold (MPT)
written by Shicheng GuoHi All, Just a simple question. Can we set Minimum MAPQ threshold to the mapping reads and Minimum Phred threshold of base in the bismark_methylation_extractor …
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Can Bowtie 0.12.7 Handle Sanger / Illumina 1.9 ?
written by fire_waterHello. I have a user that needs to use Bowtie 0.12.7 (Yeah, old version. Don't ask.) but the quality score format of our FASTQ files …
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Vcf File Format Qual Column
written by User6891<p>I'm generating a VCF file which consists of genotype data from 5 individuals. For each variant from each individual I have a Phred Quality Score. …
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Computing A Short Read'S Score
written by Raygozak<p>Hi, if i have the following read:</p> <pre><code> @HWI-ST261:7:1:16113:8289#0/1 .CTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTCCGGGAGGGGCGCATTTATTAG + BWURTY[YYVacaccccccca_ccc\cc_ccccccccac_c_aYVcccc_c_accc_ZccUUUUVYV_c_[ZVV^ </code></pre> <p>Where the 4th row is the score. as far as i understand …
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Calculation Of Average Mapping Quality Over A Given Genomic Region
written by Bioscientist<p>For a given genomic region,how can I calculate:</p> <p>1.average mapping quality(phred-like) for all mapped reads in the bam file over the region.</p> <p>2.average sequencing quality(also …
Do you have SRA data with Bustard (Illumina intermediate) files?