Question: Bowtie on Galaxy - -v or -n ?
gravatar for erica.mica
21 months ago by
erica.mica0 wrote:

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,


bowtie galaxy • 693 views
ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 21 months ago by erica.mica0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This question was asked a few years ago at seqanswers:

The option -v sets what is reported in the end, but you can also set -n to help the job run faster/use less resources for hits that will later be discarded.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k

thank you for the kind answer. what is not clear to me is why, using galaxy, the -v 0 option does not set 0 mismatches.... anyone could help?? thanks erica

ADD REPLYlink written 21 months ago by erica.mica0
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