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Question: To merge several count data into one matrix.
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gravatar for dhpark
5 months ago by
dhpark • 10
dhpark • 10 wrote:

Hello all.

I would like to merge or combine my count data into one matrix for using Degust program but I could not find the right way for it. During googling I found galaxy had 'SAM/BAM to count matrix' tool but I think it does not here anymore (or I could not find. If it is sorry about that and please let me know.). Could you tell me what should I do next for merging my data into one matrix?

Thank you for your help. Best,
columns text degust matrix rna-seq • 550 views
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modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 5 months ago by dhpark • 10
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gravatar for Jennifer Hillman Jackson
5 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You are using Degust line-command or through a web portal, correct? This prior post is still true, in short, the tool is not fully wrapped for Galaxy yet: https://biostar.usegalaxy.org/p/10966/

Tool manual and input format documentation (updated link versus prior Q&A above): http://degust.erc.monash.edu/

Tabular data (count tool output) can be merged with a few different tools, search in the tool panel with the keyword "join" to find the choices. If your count data was created in Galaxy, then you wouldn't have csv output, but a tabular format to start with and that should be retained for joining and other changes needed to get the file into the specification (content, column ordering, adding in a header line). After, tools in the group Text Manipulation can transform data in many ways, including with sed and awk for custom manipulations. Converting tabular data to cvs data does not have a distinct tool as csv format it is rarely used with wrapped Galaxy tools.

For example text manipulation/join functions, please see the Galaxy 101 tutorial: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you for your kind reply. It helps a lot. Thank you again.

ADD REPLY • link written 5 months ago by dhpark • 10
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