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Old 08-19-2013, 11:53 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077
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Quote:
Originally Posted by rzeng View Post
I used extra barcode file (6 different barcode) to split data 2 into 6 groups of different files (by galaxy barcode splitter). Now, I was stuck here and can't keep going until I figure out the following questions,

1. How can I sort the forward data1 and reverse data2 using my 6 files generated by barcode splitter. Is there software to do this? By the way, I do not have much bioinformatics background, any good suggestion?

2. How do I know where is the adapt sequences or if there are adapt sequences in the forward/reverse sequence from data 1 and 3 because this is very helpful for me to do adapt trim from original sequence?
If you managed to get the forward and reverse reads into separate files for each sample then you have made good progress. At this stage you probably want to do some QC on the files.

Here is a link for some practical info to get you started: http://en.wikibooks.org/wiki/Next_Ge...Pre-processing

As for some of other questions use the "search" functionality on this site along with clever combinations of key words. You will find many past threads that have the answers you need (and also additional info you may not have thought about to ask).
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