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sivarajankumar / fluxcapacitor

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how to generate the pair-end reads in two separate files? #39

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
I found the pair-end short reads are put in one file instead of two
separate files.
I think it would be consist with many alignment software if the Flux
Simulator can provide this feature.

Original issue reported on code.google.com by Guorong...@gmail.com on 22 May 2010 at 3:27

GoogleCodeExporter commented 8 years ago 
Dear Guorong,

actually paired-end reads come out of most sequencing machines as a single 
sequence
that joins both mates. Later-on they get split in a post-processing step. So 
far, I
did not come accross read mappers (that is what you meant by alignment software,
right?) having problems with mates being joint in a common file. However, if
necessary, you should be able to split rather easy by the suffix of the read 
name,
see also the thread about the read identifiers at

http://fluxcapacitor.wikidot.com/forum/t-242373/can-you-provide-the-document-abo
ut-the-identifier-of-reads

Original comment by gmicha@gmail.com on 26 May 2010 at 1:31