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Tag Archives: mapping
Using blat
My multipurpose sequence aligner tool of choice for many years has been blat. This is just a short post on the very basics of blat. Below is a slide I made couple of years ago: First blat splits the reference … Continue reading
bowtie and multimapping reads
I first tried this with BWA. Now I’ll try it with bowtie. Consider this reference sequence: >artificial ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG and this read: … Continue reading
Mapping random sized reads to the genome
Simple question, what are the mapping statistics for random pieces of DNA of size 10 to 30 to the human genome? Generate 1,000,000 random pieces of DNA from size 10 to 30: Map to the hg19 genome using BWA with … Continue reading
bwa and multi mapping reads
Consider this reference sequence: >artificial ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG ACGTACGTACGTACGTAGGTACGTAGGG and this read: >tag ACGTACGTACGTACGTAGGTACGTA Using bwa (Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.5.9-r1) this is the SAM output tag 0 artificial 57 0 25M * 0 0 ACGTACGTACGTACGTAGGTACGTA … Continue reading
Mapping qualities
Short read alignment programs, such as bwa, usually have a mapping quality score for each read that is aligned to a reference. I came across this useful post in seqanswers and here I try to replicate it with an example … Continue reading
Can we use blat to map miRNA’s?
From miRBase downloaded the mature miRNA’s. In the file, there are currently 1,223 miRNA’s for the human genome. Using default blat settings, 152 (133 map to only one loci) of the mature human miRNA’s can be mapped to the assembled … Continue reading