Question: Question About Using Bowtie
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gravatar for William Light
6.6 years ago by
William Light50 wrote:
I am trying to use bowtie to assign reads to the s. Cerevisiae genome. I have data from paired end SOLiD sequencing with two unique six base pair barcodes. Can I use bowtie to make csfasta and qual files from my mixed original data split by bar code? I know I can use the trim option to remove the barcode, but how do I specify one only?
alignment bowtie • 796 views
ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by William Light50
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gravatar for Jennifer Hillman Jackson
6.6 years ago by
United States
Jennifer Hillman Jackson24k wrote:
Hello William, The tools in "NGS: QC and manipulation", especially those in the sub-section "AB-SOLiD data" can do the manipulations needed before mapping. It may be helpful to view the screencast at http://usegalaxy.org, center pane, quickie #9. Hopefully this helps to get you started, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENTlink written 6.6 years ago by Jennifer Hillman Jackson24k
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gravatar for William Light
6.6 years ago by
William Light50 wrote:
I have created fixed-step wiggle files for a project that I am working on, but I am wondering if there is an easy way to transform the values by a correction factor to account for differences in in the number of reads for two different samples (one had 1.5 million or so, the other had 6.6million).
ADD COMMENTlink written 6.6 years ago by William Light50
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