about bwa aln parameter tuning questions
Hi guys,
I'm using bwa to align solexa short reads (32 bp) to the reference genome. There are a couple of parameters for 'bwa aln', some of which I can't understand well. Could someone kindly help me fix some of my concerns as follows?
The default values for parameters in bwa aln are as follows: aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -l inf -k 2 -t 1 -M 3 -O 11 - E 4
In regards to bwa aln -n, the default value for -n is 0.04, is there anyway I can know the maximum edit distance ? Why is the default value for -n set as 0.04?
In regards to -o, the default value for -o is 1. why is just one gap open allowed in one query sequence in the default setting?
In regards to -e, the default value -e is -1. why is gap extention not allowed in one query sequence in the default setting?
In regards to -l, the default value for -l is inf. why is seeding disabled in the default setting?
When I use bwa aln, do I need to tune the parameters or just use the default setting for these parametersl? If the parameters are needed to be tuned, how should I tune these parameters?
Could anyone kindly give me some suggestions?
Thank you very much!
Best
Jing
I'm using bwa to align solexa short reads (32 bp) to the reference genome. There are a couple of parameters for 'bwa aln', some of which I can't understand well. Could someone kindly help me fix some of my concerns as follows?
The default values for parameters in bwa aln are as follows: aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -l inf -k 2 -t 1 -M 3 -O 11 - E 4
In regards to bwa aln -n, the default value for -n is 0.04, is there anyway I can know the maximum edit distance ? Why is the default value for -n set as 0.04?
In regards to -o, the default value for -o is 1. why is just one gap open allowed in one query sequence in the default setting?
In regards to -e, the default value -e is -1. why is gap extention not allowed in one query sequence in the default setting?
In regards to -l, the default value for -l is inf. why is seeding disabled in the default setting?
When I use bwa aln, do I need to tune the parameters or just use the default setting for these parametersl? If the parameters are needed to be tuned, how should I tune these parameters?
Could anyone kindly give me some suggestions?
Thank you very much!
Best
Jing
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