Moderator: Mo Heydarian

gravatar for Mo Heydarian
Mo Heydarian820
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820
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Location:
United States
Last seen:
1 day, 1 hour ago
Joined:
6 years, 2 months ago
Email:
m*********@gmail.com

Posts by Mo Heydarian

<prev • 124 results • page 1 of 13 • next >
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Answer: A: Workflow inserting input name to output file
... Hi, Try using the 'Collection Column Join' tool. This tool will combine files based on a common identifier and include the file name in each column header. If your input data is: ID Col2 Col3 The output would look like: ID SRR123456_2 SRR123456_3 SRR654321_2 SRR654321_3 Also have a look at ...
written 1 day ago by Mo Heydarian820
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Answer: A: How to do differential peak analysis after scaling bam files?
... Hello, To compare your scaled bedgraph files, you could use multiGPS or SICER. Both of these tools are available on useGalaxy.org and accept bedgraph file as input to determine differential binding. You can subsequently filter out the differentially bound regions not corresponding to your peaks usi ...
written 4 weeks ago by Mo Heydarian820
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Answer: A: Increasing galaxy memory
... Hello, An increase in storage quota on useGalaxy.org can be requested by emailing galaxy-bugs@lists.galaxyproject.org with a short explanation of why you need increased storage and for how long you will need it. Thanks for using Galaxy! Cheers, Mo Heydarian ...
written 14 months ago by Mo Heydarian820
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Comment: C: mRNA expression Count
... Please follow the tutorial I provided. In the tutorial normalized counts of transcripts are generated by DESeq2. You will need to provide the reference transcriptome (GTF) corresponding to your the organism you are working with: https://genome.ucsc.edu/cgi-bin/hgTables Thanks for using Galaxy! ...
written 14 months ago by Mo Heydarian820
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Answer: A: Save my data
... Hello, If you are using Galaxy all of your input, intermediate, and output files and visualizations are saved in your history. If this is not what you are asking about, please be more specific about what your goal is. Thanks for using Galaxy! Cheers, Mo Heydarian ...
written 14 months ago by Mo Heydarian820
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Comment: C: "Fold" a column from a table?
... For the example data you posted, you could select lines matching (or not matching) "NP_" using the "Select" tool. This tool will search and select rows matching (or not) a string you provide. ...
written 14 months ago by Mo Heydarian820
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Comment: C: "Fold" a column from a table?
... Try splitting the data into two files, the first with correctly formatted data and the second with rows that have blank entries. For the second file, you can add a placeholder using "Add column" and then rearrange the columns with the "Cut" tool. Once the second file has the same format as the fir ...
written 14 months ago by Mo Heydarian820
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Answer: A: mRNA expression Count
... Hello, You can perform RNA-seq analysis in Galaxy. Most of the standard tools for RNA-seq analysis are available on useGalaxy.org Please have a look at the following tutorial that has step-by-step instructions for dealing with RNA-seq data, including sample data for trial and error: https://galaxyp ...
written 14 months ago by Mo Heydarian820
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Answer: A: "Fold" a column from a table?
... Hello, You could use the "Group" or "Datamash" tools. You would group by the first column and "concatenate distinct" on the 2nd, 3rd, and 4th columns. In the case of your example, I would clean it up to remove the 4th line, as it has a different number of columns the the first three. I'd suggest usi ...
written 14 months ago by Mo Heydarian820
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Comment: C: Trinity on Queue
... Please try rerunning these jobs. ...
written 14 months ago by Mo Heydarian820

Latest awards to Mo Heydarian

Popular Question 12 months ago, created a question with more than 1,000 views. For Installing HISAT2 on Cloudman
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: RNAseq analysis starter
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: RNAseq analysis starter
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: RNAseq analysis starter
Centurion 15 months ago, created 100 posts.
Popular Question 15 months ago, created a question with more than 1,000 views. For bedTools - Genome file
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Asking for R and XML code examples for creating Galaxy Interface.
Scholar 16 months ago, created an answer that has been accepted. For A: Asking for R and XML code examples for creating Galaxy Interface.
Popular Question 18 months ago, created a question with more than 1,000 views. For bedTools - Genome file
Scholar 22 months ago, created an answer that has been accepted. For A: cuffdiff conditions related question
Scholar 2.1 years ago, created an answer that has been accepted. For A: cuffdiff conditions related question
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: cuffdiff conditions related question
Supporter 2.1 years ago, voted at least 25 times.

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