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Old 03-09-2015, 04:50 AM   #45
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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@Elsie: Are you trying to analyze NextSeq500 data or just creating stats? This thread was originally about quality of NextSeq500 reads and the procedure that Brian had posted was to create stats files (not actual alignments).

If you are actually trying to analyze real data then there is no need to create interleaved data sets. You can directly trim and then align R1/R2 reads against human genome. You need to specify an output file to store the aligned reads.

A minimal command line for doing the mapping would be following. More examples in the BBMap thread: http://seqanswers.com/forums/showthread.php?t=41057
Code:
$ bbmap.sh -Xmx30g in=trimmedfq.gz path=/path_to_BBMap_index_top_folder_with_ref_directory/ out=sample_ID.sam qin=33
Change the path to BBMap index according to your local path. Add additional options (there are plenty) as needed depending on kind of experiment you are analyzing.
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