Question: Map with Bowtie for Illumina
gravatar for tima
4.4 years ago by
United States
tima0 wrote:

Hi All,

question about "Map with Bowtie for Illumina" tool,

if read maps to multiple locations on the chromosome (for ex. ribosomal RNA genes), will it be mapped to particular location or to all locations?


mapping bowtie illumina • 1.5k views
ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by tima0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The equally 'best' hits are retained (if you didn't alter the settings to retrain secondary hits). Bowtie2 has more options. Filtering with SAMTools after mapping, to only keep properly mapped pairs, may be done if needed with either (or any SAM/BAM file).

Best, Jen, Galaxy team

ADD COMMENTlink written 4.4 years ago by Jennifer Hillman Jackson25k
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