Hi,
What are the disadvantage of local alignment mode in bowtie2?
We have a data set with very high quality reads. But when running...
10 results in 0.0024 seconds.
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bowtie2 local alignment
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gaps in calculating mapping quality
Hi all,
I am new to this field and I am having trouble figuring out how mapping quality is calculated for gapped alignments. I looked up... -
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 Reports High Mapping Quality for Poorly Mapped Pairs
I realized after I, serendipitously, ran "bwa sampe" on the same identical alignments (i.e. sai files from the same fastq) that the second mate... -
IGV: Mapping Quality vs. XA tag (I'm lost)
Hello all,
In IGV, reads with a mapping quality = 0 are displayed in white while reads
with a positive mapping quality are displayed... -
pileup output format
Hey guys, I went through pileup format specifications on the website many times, but still have some silly questions. Would you please give me some hints?... -
Question about BWA mapping quality
I need to verify that BWA takes into account mate pair data, and the BWA paper that I found seems to be somewhat ambiguous in how it derives mapping quality... -
mapping quality score in tophat sam file
Hello all,
I have been trying to work with the sam output file that I received from tophat. My input file was an RNA-sequencing... -
What's left of 5 million reads
Hi,
I'm working with Illumina GAII data (5 million reads) from a 5' cap capture library. I did the mapping against a transcriptome with ELAND_standalone... -
BWA paired end mapping quality
I used BWA to map my PE sequencing data to reference genome. I try to use paired mapping quality to filter bad read pairs out for downstream analysis....
