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Old 09-08-2014, 12:03 PM   #1
Location: UK

Join Date: Feb 2014
Posts: 60
Default No BWA alignment output files!


I have been using Bowtie for the last few months for alignment but now have a file for indexing which is 6Gb and Bowtie cannot deal with so I have moved onto using BWA, the indexing went fine and I got my files.

When reading the documentation is seemed as though "bwa mem" was the best option for the actual alignment however all the output is being sent to the screen and now an actual file (determined as iy is going to the output file from the cluster we have and no new files have been created).

Basically was this the correct choice and did I miss something which has caused the output of aligned and unaligned files to not be created?

here is the code I used:

bwa index -p 50Gb_index -a bwtsw contigs.fa

bwa mem -t 20 50Gb_index ../../NZ_bowtie_nonaligned_hungate_thread.done.gz

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