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Question: Map with Bowtie for Illumina
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gravatar for tima
4.4 years ago by
tima • 0
United States
tima • 0 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?

thanks.
mapping bowtie illumina • 1.5k views
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modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by tima • 0
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gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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