I've been searching the forum for an answer for this, but couldn't find exactly what I was looking for. If a thread answering my question already exists, I would be grateful if someone pointed me to it.
So, I've been trying out bwa for mapping of 75bp mate-pair Illumina data. It works fine so far, but I was trying out various parameters in bwa aln to find out the best setting and I think I need a little help.
I've been playing with the parameters -n -q -k and -l and what I basically wanted to achieve is to allow only one or two mismatches per read. I've tried to disable seeding by setting a very high value for -l and then setting -n 1 or 2, but in IGV I can still see some reads that have a lot more mismatches.
The last I tried out was:
-n 2 -k 1 -l 10 -q 15
but still I see reads with more than 2 mismatches...
I would be very interested in why there are still more mismatches in my reads than I thought I allowed and also if you have some examples of parameters that you use for bwa Illumina mapping. I know it depends on the project etc. (like using -q 15 only if many of your reads have bad quality towards the end) but it would be good to get an idea what other people use concerning seeding/no seeding/number of mismatches etc.
Thanks in advance!
So, I've been trying out bwa for mapping of 75bp mate-pair Illumina data. It works fine so far, but I was trying out various parameters in bwa aln to find out the best setting and I think I need a little help.
I've been playing with the parameters -n -q -k and -l and what I basically wanted to achieve is to allow only one or two mismatches per read. I've tried to disable seeding by setting a very high value for -l and then setting -n 1 or 2, but in IGV I can still see some reads that have a lot more mismatches.
The last I tried out was:
-n 2 -k 1 -l 10 -q 15
but still I see reads with more than 2 mismatches...
I would be very interested in why there are still more mismatches in my reads than I thought I allowed and also if you have some examples of parameters that you use for bwa Illumina mapping. I know it depends on the project etc. (like using -q 15 only if many of your reads have bad quality towards the end) but it would be good to get an idea what other people use concerning seeding/no seeding/number of mismatches etc.
Thanks in advance!
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