Hi,
We're planning on using the Mortazavi ERANGE package for quantifying gene expression in our rna-seq data. An aligner must be used for this process, and we are going to use Bowtie.
The ERANGE documentation describes how Bowtie should be used to create output that is compatible with the ERANGE process, but part of it is confusing me:
My understanding is that the "-m 10" will make the "-k 11" non-sensical, since any reads with more than 10 matches will be discarded, therefore making it impossible to report up to 11.
Have I misunderstood?
Thanks!
We're planning on using the Mortazavi ERANGE package for quantifying gene expression in our rna-seq data. An aligner must be used for this process, and we are going to use Bowtie.
The ERANGE documentation describes how Bowtie should be used to create output that is compatible with the ERANGE process, but part of it is confusing me:
We use the following settings to emulate Eland output:
$BOWTIEDIR/bowtie zzz -v 2 -k 11 -m 10 -t --best -f s1.32mer.query.txt --unfa s1.unmapped.fa --maxfa s1.repeat.fa s1.zzz.bowtie.txt
where zzz is the genome prefix that you gave when building the
genome. In particular, we ask bowtie to map all multireads up
to 11 ("-k") with up to 2 mismatches ("-v" and "--best"), however
we will only import all multireads up to 10x multiplicity ("-m").
$BOWTIEDIR/bowtie zzz -v 2 -k 11 -m 10 -t --best -f s1.32mer.query.txt --unfa s1.unmapped.fa --maxfa s1.repeat.fa s1.zzz.bowtie.txt
where zzz is the genome prefix that you gave when building the
genome. In particular, we ask bowtie to map all multireads up
to 11 ("-k") with up to 2 mismatches ("-v" and "--best"), however
we will only import all multireads up to 10x multiplicity ("-m").
My understanding is that the "-m 10" will make the "-k 11" non-sensical, since any reads with more than 10 matches will be discarded, therefore making it impossible to report up to 11.
Have I misunderstood?
Thanks!
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