Good morning, I'm using Galaxy with Bowtie for Illumina to map smallRNA sequencing (illumina) on a short sequence coming from my reference genome, to visualize the distribution of my reads on a genome area of interest (5 kb).
I want to set Bowtie in order to have zero mismatches. How should I set the parameters? I have tried -v = 0, but I still have 2 mismatches allowed.
Here are all the parameters used.
Bowtie settings to use full
Skip the first n reads (-s) 0
Only align the first n reads (-u) -1
Trim n bases from high-quality (left) end of each read before alignment (-5) 0
Trim n bases from low-quality (right) end of each read before alignment (-3) 0
Maximum number of mismatches permitted in the seed (-n) 2
Maximum permitted total of quality values at mismatched read positions (-e) 70
Seed length (-l) 28
Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround) Round to nearest 10
Number of mismatches for SOAP-like alignment policy (-v) 0
Whether or not to try as hard as possible to find valid alignments when they exist (-y) Do not try hard
Report up to n valid alignments per read (-k) 1
Whether or not to report all valid alignments per read (-a) Do not report all valid alignments
Suppress all alignments for a read if more than n reportable alignments exist (-m) -1
Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max) False
Write all reads that could not be aligned to a file (--un) False
Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best) noBest
Maximum number of backtracks permitted when aligning a read (--maxbts) 125
Override the offrate of the index to n (-o) -1
Seed for pseudo-random number generator (--seed) -1
Suppress the header in the output SAM file False
Job Resource Parameters no
Should I set -n=0 and also -v=0 ? I have tried this option and it seems it works, but I am not sure it is correct. I know that -v and -n options are usually exclusive.
thank you for any help,
Erica
