Hi everybody,
maybe I misunderstood it completely, but what is the option -m good for?
If I am looking for differentially regulated genes in my data set and i set a high m-value (lets say 5), I know there are for some reads up to five different possible locations which they can be matched.
@what exactly does it mean for my data?
Do I have my read at different positions on the reference genome?
This way my data for differentially expressed genes will be biased.
Do I have these reads at five locations or there is just one, best location where it mapped to.
I have pair-end data set, so I can't use the best and strata combination.
@What I don't exactly understand is the definition of uniqueness in the bowtie -m option?
If I use the option -m 1 I will loose a large part of my data, so I don't want to do it, but I would like to see, that the reads are mapped are as specific as possible.
the command I use to run bowtie is as such:
maybe I misunderstood it completely, but what is the option -m good for?
If I am looking for differentially regulated genes in my data set and i set a high m-value (lets say 5), I know there are for some reads up to five different possible locations which they can be matched.
@what exactly does it mean for my data?
Do I have my read at different positions on the reference genome?
This way my data for differentially expressed genes will be biased.
Do I have these reads at five locations or there is just one, best location where it mapped to.
I have pair-end data set, so I can't use the best and strata combination.
@What I don't exactly understand is the definition of uniqueness in the bowtie -m option?
If I use the option -m 1 I will loose a large part of my data, so I don't want to do it, but I would like to see, that the reads are mapped are as specific as possible.
the command I use to run bowtie is as such:
bowtie -a -m 5 -n 2 -l 22 -q --un total_trimmed.unmapped -t -p 2 -5 11 --chunkmbs 256 --max total_5trimmed.maxHits -S d_melanogaster_fb5_32 -1 s2_1_sequence.fq -2 s2_2_sequence.fq total_5trimmed.sam
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