I had found very confused FastQC report for Rick’s miRNAseq experiment. I did not understand and wanted to confirm what I have seen.

I downloaded the data in Kuchen, S et al paper on GenomeResearch, 2010. Using SRR042443.sra as an example to evaluate the data quality. Detail see command_01112013.txt

Using SRR042443.fastq as an example

Step 1: fastq-dump to unzip the data: 
Step 2: fastQC analysis
Step 3: I saw similar results as our in-house, but I did not see the level of "over-represented sequence" matched 100% to RNA PCR primer sequences.
Step 4: Discussed with Adam, David and Pierre and decided to perform "adapter" sequencing trimming.

Strategy:

Step 1. Remove "primer sequence" by JYL (fastx-toolkit) or by AB (cutadapt)
Step 2. Align to miRBase (failed with Primer Sequence removed input file)
Step 3. Test alignment with raw file, while trying to figure out the error.

Garmire, L.X. et al report a comprehensive evaluation on eight different normalization procedures.

Case I, I wanted to create a show “Desk Top” button on the toolbar.

Solution: here is a very good tutorial link 

Follow step-by-step instruction at MiroPipeline and use Glazov, EA, Cottee PA, Barris WC, Moore RJ et al. data published: A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res 2008 Jun;18(6):957-64. PMID: 18469162

Using sra-toolkit of ncbi help link to process .sra file

It seems that the pipeline is too old to be worth tried out. At least, it provides a routine to process the miRBase .fa files.

Let’s follow the main steps and adapt it to new convention.

MGI_12172012

java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.BundleManager -- --list-install
java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.BundleManager --
--list-workflow-params --workflow-accession 7 > workflow.ini


java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher --  --ini-files workflow.ini  --workflow-accession 7 --schedule --parent-accession 24

java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.Metadata -- --list-tables
java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.Metadata -- --table study --list-fields
java -jar  SeqWare/seqware-pipeline-0.12.5.jar -p net.sourceforge.seqware.pipeline.plugins.WorkflowRunReporter -- -wa 7

nning Plugin: net.sourceforge.seqware.pipeline.plugins.BundleManager
Setting Up Plugin: net.sourceforge.seqware.pipeline.plugins.BundleManager@21f8c6df
=====================================================
===============INSTALLED WORKFLOWS===================
=====================================================
Name    Version Creation Date   SeqWare Accession       Bundle Location
-----------------------------------------------------
FileImport      0.1.0   Wed Jan 04 13:51:00 EST 2012    4       null
First           Fri Nov 30 16:17:31 EST 2012    15      null
HelloWorldWorkflow      1.0     Wed Aug 15 19:00:11 EDT 2012    7       /home/seqware/SeqWare/released-bundles/Workflow_Bundle_H
elloWorldWorkflow_1.0_SeqWare_0.12.5.zip

FPKM data was provided by Sara at: /ddn/gs1/project/mousemeth/RNAseq/analysis/sara/rnaseq_analysis_Aug2012/vs_mm9/cufflinks

Now, I need created links to those files. The command log is saved as: /ddn/gs1/home/li11/project2012/ASE/FPKM_RNAseq/command_12102012.txt