UAB Galaxy RNA Seq Step by Step Tutorial

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(Upload data)
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== Upload data ==
 
== Upload data ==
* specify organism (request or include fasta if not in list)
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* QC check
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For this tutorial, we will have 2 samples, sequences with paired-end reads. That gives us 4 FASTQ files to upload.
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=== set filetype and genome ===
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To start, you must move the data (FASTQ) from the sequencing center into the Galaxy instance, be sure to specify the filetype (fastqsanger for UAB and HudsonAlpha) and the organism that was sequenced ("Genome database"), in this tutorial, "mm9" for mouse.
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=== check quality of data ===
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At this step, we check the quality of sequencing. This says nothing about the quality of the sample, or whether it was the right sample. We'll check that later.
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. This
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== Align using TopHat ==
 
== Align using TopHat ==
  

Revision as of 13:40, 13 September 2011

Contents

Galaxy RNA-Seq Step-by-Step Tutorial/Protocol

Upload data

For this tutorial, we will have 2 samples, sequences with paired-end reads. That gives us 4 FASTQ files to upload.

set filetype and genome

To start, you must move the data (FASTQ) from the sequencing center into the Galaxy instance, be sure to specify the filetype (fastqsanger for UAB and HudsonAlpha) and the organism that was sequenced ("Genome database"), in this tutorial, "mm9" for mouse.


check quality of data

At this step, we check the quality of sequencing. This says nothing about the quality of the sample, or whether it was the right sample. We'll check that later.

. This

Align using TopHat

QC alignment

* %mapped
* visualize in IGV or IGB

Construct transcripts : Cufflinks

* Denovo vs existing annotation
* UAB Modified Reference annotations

Compare transcript levels: cuffdiff/cuffcompare

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