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Hi,
I have ~35000000-40000000 mate pair reads per sample (2 fastq files with 35e6 reads per cell line) which I need to map. MAQ is the most sensitive (to my knowledge) but have this 2000000 reads restriction. bwa is good and fast but general opinion is that , after bwa, one would like to map discordant pairs with MAQ. And common opinion is that bowtie is not appropriate for long
insert pairs (that is mate pair sequencing data). BTW bwa requires
reverse complement of the fastq files (for mate-pairs) and I am not sure
that quality weights bwa is supposed to assign depending on nucleotide
position are applicable. How about novocraft? can someone advice me on this? Thank you.
I have ~35000000-40000000 mate pair reads per sample (2 fastq files with 35e6 reads per cell line) which I need to map. MAQ is the most sensitive (to my knowledge) but have this 2000000 reads restriction. bwa is good and fast but general opinion is that , after bwa, one would like to map discordant pairs with MAQ. And common opinion is that bowtie is not appropriate for long
insert pairs (that is mate pair sequencing data). BTW bwa requires
reverse complement of the fastq files (for mate-pairs) and I am not sure
that quality weights bwa is supposed to assign depending on nucleotide
position are applicable. How about novocraft? can someone advice me on this? Thank you.