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Old 12-09-2010, 12:08 PM   #1
Location: Woods Hole, Massachusetts

Join Date: Jul 2010
Posts: 16
Default BWA aligner - zebrafish miRNA


I have couple of questions with regard to SOLiD reads and BWA aligner for analyzing zebrafish miRNA results.

1. I am using BWA to align my reads and I do not get any unique reads. I am not sure if this has something to do with indexing zebrafish genome. They are couple of different fasta (.fa) files available for download.

a) danRer6.fa.gz - "Soft-masked" assembly sequence in one file.
Repeats from RepeatMasker and Tandem Repeats Finder (with period
of 12 or less) are shown in lower case; non-repeating sequence is
shown in upper case. (I tried this one)

b) danRer6.fa.masked.gz - "Hard-masked" assembly sequence in one file.
Repeats are masked by capital Ns; non-repeating sequence is shown in
upper case.

c) danRer6.fa.out.gz - RepeatMasker .out file. RepeatMasker was run with the -s (sensitive) setting.

Which one of these is the correct one to use?

Second question I am having is 2) what options to use for bwa aln (I tried bwa aln -n 3 -t 2) to delete bad reads.

Any help will be really helpful.

Thank you
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