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Question: Need help with "Bowtie2" tool
1
gravatar for meltemelitas
4.3 years ago by
meltemelitas • 10
United States
meltemelitas • 10 wrote:

Although my fasq data is in loaded, why could I not see the fast file in the bowtie2 checkbox?

Thanks!

 

Tool name: Bowtie2
Tool version: 0.2
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.2
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/bowtie2

 
fastq datatype metadata rna-seq bowtie2 • 1.1k views
ADD COMMENT • link •
modified 4.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by meltemelitas • 10
1

What is a fast file and to which checkbox do you refer?

 

ADD REPLY • link written 4.3 years ago by Bjoern Gruening ♦ 5.1k

Thank you very much, it was a fastq RNA-sequencing data file. When i try to use Bowtie2, I supposed to see the fasq file that I uploaded and visible in the history section.

If It is not clear, I can send an image of the screen.

Thank you very much! I appreciated!

ADD REPLY • link written 4.3 years ago by meltemelitas • 10
0
gravatar for Jennifer Hillman Jackson
4.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

Here is some help for permitting tools to recognize datasets:
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

And be certain that the formatting is correct, especially for fastq datasets. Proper quality score scaling and datatype assignment is very important:
http://wiki.galaxyproject.org/Support#Dataset_special_cases -> see FASTQ in first section

Your question was a bit difficult to understand, so please let us know if this doesn't help, Jen, Galaxy team
ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k
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