Moderator: Mo Heydarian

gravatar for Mo Heydarian
Mo Heydarian690
Reputation:
690
Status:
Trusted
Location:
United States
Last seen:
3 days, 14 hours ago
Joined:
4 years, 11 months ago
Email:
m*********@gmail.com

Posts by Mo Heydarian

<prev • 104 results • page 1 of 11 • next >
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Answer: A: No Cufflinks data
... Hello, Trinity will output transcript sequences in fasta format. You can use these sequences as a reference for tools to quantify transcript expression levels. Perhaps you could try using Salmon to quantify expression levels. You should always do QC on your samples. Good luck hunting for your ph ...
written 9 days ago by Mo Heydarian690
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Answer: A: singlecell RNAseq normalisation
... Hello, There are currently no tools on useGalaxy.org to deal with spike-in based normalization. We hope to change this soon. In your case you may want to perform some additional normalization in addition to normalizing to your spike-in. Have a look at the normalization methods and packages discus ...
written 9 days ago by Mo Heydarian690
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Answer: A: No Cufflinks data
... Hello, Can you provide some more information on your pipeline? Did you map your reads to a genome? Please have a look at the tutorials here for recommended pipelines to use for RNA-seq analysis: http://galaxyproject.github.io/training-material/topics/transcriptomics/ Thanks for using Galaxy! Che ...
written 10 days ago by Mo Heydarian690
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Answer: A: Paired End FASTQ files
... Hello, If you have paired end reads you can go ahead and provide the "_1" and "_2" (or "F" and "R") pairs to Bowtie2. Typically you can use the default paired end options of Bowtie2, then modify these settings if the initial run produced poor mapping (or unexpected downstream results). If you hav ...
written 10 days ago by Mo Heydarian690
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Answer: A: RNAseq analysis starter
... Hi Bassam, If you have links to the files you can add them with the "Paste/Fetch data" option in the upload portal. If you would like help setting up a FTP connection, please see this guide: https://galaxyproject.org/ftp-upload/ Thanks for using Galaxy! Cheers, Mo Heydarian ...
written 10 days ago by Mo Heydarian690
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Answer: A: RNAseq analysis starter
... Hello, Have a look at the tutorials on transcriptomics from the Galaxy Training Network: http://galaxyproject.github.io/training-material/topics/transcriptomics/ There are two tutorials there, one for reference based RNA-seq analysis and another for de novo transcriptome reconstruction RNA-seq ana ...
written 11 days ago by Mo Heydarian690
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Answer: A: TopHat tool missing?
... An additional option for mapping RNA-seq reads is the tool RNA Star. HISAT2 and RNA Star have similar performance and accuracy on high quality libraries. RNA Star provides more robust alignments on lower quality libraries (or ones with high levels of polymorphisms) than HISAT2. For further informa ...
written 24 days ago by Mo Heydarian690
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Answer: A: Cut duplicates in Galaxy? as in Excel?
... Hello, The tool "Unique" (under the Text Manipulation category) will remove duplicate lines in Galaxy. Thanks for using Galaxy! Cheers, Mo Heydarian ...
written 7 weeks ago by Mo Heydarian690
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Answer: A: How to use and program Galaxy to download 300 SRA files at once form the NIH dat
... Hello, Great question. At the moment the best way to retrieve data from NCBI in Galaxy is by using the "NCBI SRA Tools" suite. These tools allow you to import individual data entries or import many data entries as a "collection" ready for batch analysis. I am putting a short guide below that will w ...
written 9 weeks ago by Mo Heydarian690
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Answer: A: rna seq read cleaning
... Hello, Can you provide some more information on what data you would like to remove bacterial reads from and what your desired outcome is? This will help in answering your question. Look forward to hearing from you again! Thanks for using Galaxy! Cheers, Mo Heydarian ...
written 11 weeks ago by Mo Heydarian690

Latest awards to Mo Heydarian

Teacher 10 days ago, created an answer with at least 3 up-votes. For A: RNAseq analysis starter
Centurion 10 days ago, created 100 posts.
Popular Question 17 days ago, created a question with more than 1,000 views. For bedTools - Genome file
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Asking for R and XML code examples for creating Galaxy Interface.
Scholar 7 weeks ago, created an answer that has been accepted. For A: Asking for R and XML code examples for creating Galaxy Interface.
Popular Question 12 weeks ago, created a question with more than 1,000 views. For bedTools - Genome file
Scholar 6 months ago, created an answer that has been accepted. For A: cuffdiff conditions related question
Scholar 10 months ago, created an answer that has been accepted. For A: cuffdiff conditions related question
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: cuffdiff conditions related question
Supporter 10 months ago, voted at least 25 times.

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