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How To Find The Strand-Specific Info In The Public Data From The Illumina Human Body Map 2.0 Project

Hi,

Anyone can guide a while how to find if this public rnaseq data are prepared by strand-specific assay. Thanks a lot!

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30611

Ch

rna-seq
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updated by matted matted • written by camelbbs camelbbs

I have sent an email to the submitter, hopefully she will respond here.

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written by Istvan Albert Istvan Albert

1 answer

If you read the PDF at the bottom of the page you linked, you will find the answer to your question (page 15):

"The samples used for the 2X50 and 1X75 bp runs are prepared using the Illumina mRNA-Seq kit.

– They are made with a random priming process and are not stranded."

"The sample prep used for the 1X100 bp run is the Illumina Pre- Released Directional RNA-Seq protocol.

– These data are stranded."

In general, you can usually make a quick guess by loading up aligned reads in some viewer and looking for agreement (or differences) between strands. You could also imagine doing something more sophisticated like looking at a correlation coefficient across binned read counts between the two strands... higher would indicate unstranded and lower would indicate strand-specificity.

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written by matted matted

The mind boggling part is that one needs to go to the 15th page of an associated PDF. Whereas the file itself is hosted on a supposedly science oriented website that is full of seemingly useless information:

Overall design    

Experimental Design: organism_part_comparison_design
Experimental Design: co-expression_design
Experimental Design: optimization_design
Experimental Factor Name: ORGANISMPART
Experimental Factor Name: LIBRARYPREP
Experimental Factor Name: PHENOTYPE
Experimental Factor Type: organism_part
Experimental Factor Type: protocol
Experimental Factor Type: phenotype
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written by Istvan Albert Istvan Albert

Thanks. I wonder how to look for the agreement or differences between strands in IGV browser with input bam files.

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written by camelbbs camelbbs

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