Questions tagged [read-mapping]
When dealing with associating sequencing reads to a matching position in a set of reference sequences (typically a genome).
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How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?
This is a problem I have to solve frequently, and I'd be interested in knowing what other methods people use to solve the same problem.
About twice a year, I get asked to determine variants from ...
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Why is bwa-mem the standard algorithm when using bwa?
The industry standard for aligning short reads seems to be bwa-mem. However, in my tests I have seen that using bwa backtrack (bwa-aln + bwa-sampe + bwa-samse) performs better. It is slightly slower, ...
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How does the BWA-MEM algorithm assign its mapping qualities?
Is there any resource (paper, blogpost, Github gist, etc.) describing the BWA-MEM algorithm for assigning mapping qualities? I vaguely remember that I have somewhere seen a formula for SE reads, which ...
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Library for computing BWT-based alignments
I am writing a software tool to which I would like to add the ability to compute alignments using the efficient Burrows-Wheeler Transform (BWT) approach made popular by tools such as BWA and Bowtie. ...
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Difference between BWA-backtrack and BWA-MEM
Many of my colleagues recommend I use BWA-MEM instead of regular old BWA. The problem is I don't understand why and reading the BWA man page doesn't seem to help the matter.
What is the difference ...
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How to interpret contig-alignment.psa produced by velvet
I'm using velvet to align given reads of RNA to given CDSs (i.e. coding areas and genes) of an organism, so I can generate gene-expression profiles. But after using ...
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Hisat2 : which option should mention for strand specific library read
I was trying hisat2 I get confused by the strand options...
The question has been already asked on github here but didn't get any satisfactory answer.
I'm surprise how much this strand information ...
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How to detect mismatch before mapping in RNA-Seq data
In the methods of this paper, the authors say:
Reads were then filtered based on quality score in the UMI region. Any read with >1 low-quality base (phred <=10) were discarded. Reads with more ...
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Merging/concatenating index files
I was wondering if any one has had success merging pre-generated reference index files for BWA, bowtie2 from multiple references?
For a concrete example I have hg19 and a bunch of viral and ...
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