Question: No chicken reference genome (galGal4) for Bowtie2 - map reads against reference genome
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gravatar for d92b41001
3.6 years ago by
d92b410010
United States
d92b410010 wrote:

Hi,

I cannot find the chicken (galGal4) reference genome when I run Bowtie2 - map reads against reference genome under NGS: Mapping. Could Galaxy add galGal4 Bowtie 2 inddex? Many thanks.

Gary

bowtie chip-seq • 1.1k views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by d92b410010
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gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This is on our to-do list. The time-frame is not definitive yet. For now, use the Custom reference genome feature.

Best, Jen, Galaxy team
 

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k

Hi Jennifer,

Thanks for your information. Only chicken galGal4 reference genome downloaded from UCSC is enough? Bowtie2 needs a bowtie2 index. Does Galaxy will perform it based on the custom reference genome? Thanks a lot.

Gary

ADD REPLYlink written 3.6 years ago by d92b410010
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