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Old 01-12-2012, 04:45 PM   #1
modocthegreat
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Default pair reads vs single reads

Hi,
I am very new to deep sequencing. I have a small project using RNA seq data
SRA010053 (mouse fibroblasts), SRA040235 (mouse ES cells). I was told that one of these contains paired reads. Is there some way of telling which one, just by the naming? I also have not figured out which one it is from researching the experiments. Could someone help me out here?

Thanks,
Barry
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Old 01-12-2012, 05:08 PM   #2
gringer
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SRA010053 explicitly mentions single-end reads on the project page:

http://www.ncbi.nlm.nih.gov/sra?term=SRA010053

Quote:
Sequencing of the RNA-seq shotgun library was done on an Illumina Genome Analyzer, yielding 36bp single-end reads.
But SRA040235 also mentions a layout of 'SINGLE' on the project page ('Library' section), which the SRA handbook tells me means unpaired reads:

http://www.ncbi.nlm.nih.gov/sra?term=SRA040235
http://www.ncbi.nlm.nih.gov/books/NB...ort=objectonly

So it looks like they"re both single-end from the project pages.
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Old 01-12-2012, 05:46 PM   #3
modocthegreat
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I will ask the source for a clarification. Thanks for helping me.
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