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Old 09-11-2015, 11:41 AM   #6
danova
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Location: France

Join Date: Sep 2010
Posts: 27
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Brian,
That was really great and worked as expected, however i need more control over the alignements. How can you count the number of mismatches (limit to 3 mismatches, with no indels)

Have tried also bbduk but get only small number of aligned sequences (419). I expect at least 60% of my database to match this primer.
Executing jgi.BBDukF [in=ALL16s_GOLD_HOMD.fa, out=matching.fasta, literal=CCTACGGGNGGCWGCAG, k=17, mm=f, copyundefined=t]

BBDuk version 35.43
Initial:
Memory: max=29020m, free=28565m, used=455m

Added 8 kmers; time: 0.018 seconds.
Memory: max=29020m, free=28263m, used=757m

Input is being processed as unpaired
Started output streams: 0.012 seconds.
Processing time: 0.239 seconds.

Input: 12551 reads 19118812 bases.
Contaminants: 12132 reads (96.66%) 18494334 bases (96.73%)
Result: 419 reads (3.34%) 624478 bases (3.27%)

Time: 0.275 seconds.
Reads Processed: 12551 45.59k reads/sec
Bases Processed: 19118k 69.45m bases/sec

Last edited by danova; 09-11-2015 at 12:43 PM.
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