Hi,
I have been reading Seqanswers for quite some time, but this my first question.
Does someone has experience with BAM...
13 results in 0.0030 seconds.
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UCSC Encode files issue with MAPQ and Flags
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Reassign mapping quality in STAR / GATK/ Cufflinks compatibility
Hello all,
I'm reassigning mapping quality values produced by STAR from 255 to 60 (column 5 of the output) for GATK compatibility and I... -
Bowtie2 and MapQ Calculation
Hi
I'm going to ask about bowtie2's mapping quality calculation for ChIP-Seq data. For sequences which align multiple locations Bowtie2...Last edited by KyuzoSeq; 03-08-2015, 05:47 AM. -
How BWA and Bowtie mention unique reads in SAM files?
Hello everybody,
I am trying to figure how BWA and Bowtie define a read as unique.
Making here an algorithm to decide if a read... -
How is the p-value for MAPQ calculated in Bowtie2?
Hi everyone,
I would like to obtain some kind of metric that represents how uniquely a sequence maps to the genome. Similar, in principle,... -
picard SamToFastq error in umapped reads which MAPQ is not 0
Hi,
SamToFastq.jar will be stop when it meet the unmapped reads which flag is 4 or 20 but the MAPQ is not 0. Picard is not so smart,it couldnot...Last edited by upper; 12-05-2012, 05:33 PM. -
BWA MAPQ=0 with one best hit
Hello
I was trying to understand the mapping quality genererated by BWA. I put all the data in xxx.sam into MySQL DB, and investigated each Tag... -
A question about the MAPQ (mapping quality) in SAM file
hey everyone,
I am looking into a SAM file now and found the MAPQ field all filled with 255. 255 means mapping quality not available, right?... -
samtools view and mapq
I am working with paired end Illumina resequencing data from multiple populations.
My workflow involves samtools view -q to generate bamfiles... -
bowtie2 quality scores same for every read
Dear all,
I am trying to map Illumina 2x126bp exome data (Nimblegen v3) with bowtie2. Subsequently, I want to perform variant detection... -
bwa: “XT:A:U” and MAPQ of 0 at the same time
I map RNA-Seq Data with BWA to the genome. The output files from BWA in sam-format contain reads that have on the one hand the tag "XT:A:U"... -
bwa vs bowtie filtering parameters
I recently switched from using bwa to using bowtie for aligning reads to hg19. Using bwa I filtered out MAPQ score below 30. This seems like a fairly... -
filtering for uniquely mappable regions
I have paired end 101 bp reads for some yeast strains. I am currently using bwa to map reads and the GATK to call and filter SNPs and indels. For various...Last edited by dphansti; 10-06-2011, 03:40 PM.
