Hi,
I try to map relatively long reads (80-bases-long single read, fastq format) to hg19 using bowtie.
Does anybody tell me which parameters should be modify for this kind of mapping ?
I used
bowtie -p 4 --best --strata -m 1 --sam /index_hg19 -q 80_mer_read.fastq output.sam
I may forget some important parameters to be changed.
Thanks,
I try to map relatively long reads (80-bases-long single read, fastq format) to hg19 using bowtie.
Does anybody tell me which parameters should be modify for this kind of mapping ?
I used
bowtie -p 4 --best --strata -m 1 --sam /index_hg19 -q 80_mer_read.fastq output.sam
I may forget some important parameters to be changed.
Thanks,
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