Question: Tophat vs Bowtie2
0
gravatar for pattythepsuwan
4 months ago by
pattythepsuwan0 wrote:

Hello,

I took the fasq files and ran Tophat then Bowtie2. Is it okay to run tophat first then bowtie2 or in reverse order. Please advice.

Best, Patty Thepsuwan

rna-seq tophat bowtie bam • 132 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by pattythepsuwan0

What is your goal?

Bowtie is for mapping DNA and sometimes very short or unspliced RNA.

Tophap is for mapping spliced RNA. Note that this tool has been deprecated (and will soon be removed again from http://usegalaxy.org). Using HISAT (or RNASTAR) instead is highly recommended.

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson23k
0
gravatar for pattythepsuwan
4 months ago by
pattythepsuwan0 wrote:

Hi Jennifer,

I am trying to analyze the Ribo-seq data. I cannot find any program that analyze the ribo-seq. However, I begin by using the RNA-seq analysis and first thing I do is mapped the data into BAM file. Any modules on Galaxy that recommend to use with Ribo-seq analysis? Also I am very new to the Galaxy community and still learning. Thank you for all the help.

Sincerely, Patty Thepsuwan

ADD COMMENTlink written 4 months ago by pattythepsuwan0
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