Can someone explain to me what the orientation in paired-end RNA-seq data means? Is forward/forward the standard orientation? How does this affect tophat options, just specify unstranded Rna-seq?
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If you are only looking for a primer on the "paired end" part have a look at this blog entry: http://www.homolog.us/blogs/blog/201...looking-reads/ You are less likely to have the second kind of libraries mentioned in the post.
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Originally posted by puggie View PostWhat protocol did you use for library preparation? Normally for ScriptSeq Illumina libraries, the forward reads would correspond to the DNA coding strand while the reverse reads would be reverse complements,
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I'm not sure what the 'standard orientation' is.
But if you want to know more about read-orientation then take a look at these threads:
Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc
And while 'unstranded' is the default mode for tophat/bowtie, you need to change that if your library is something else.
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Originally posted by Nick View PostI'm looking at this SRA entry
http://www.ncbi.nlm.nih.gov/sra?term=SRX142112
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