I will be very obliged if someone can help me with this question. I am new to the field of mapping reads with next gen sequencing.
I have Sanger reads 80-150 bp and I am using BWA to align my reads to the human genome. In the output of my results I get reads that are mapped to multiple locations, but the results have only one position returned (best hit). How do I get all the hits returned in my output.
Here are the parameters I have used:
bwa aln -n 0.10 -o 3 -M 1 -O 5 -E 1 /home/data/chr8_all.fa /home/data/data1.fastq > /home/data/data1_aln_sa.sai
bwa samse chr8_all.fa data1_aln_sa.sai data1.fastq > data1_aln.sam
Thanks
biobee
I have Sanger reads 80-150 bp and I am using BWA to align my reads to the human genome. In the output of my results I get reads that are mapped to multiple locations, but the results have only one position returned (best hit). How do I get all the hits returned in my output.
Here are the parameters I have used:
bwa aln -n 0.10 -o 3 -M 1 -O 5 -E 1 /home/data/chr8_all.fa /home/data/data1.fastq > /home/data/data1_aln_sa.sai
bwa samse chr8_all.fa data1_aln_sa.sai data1.fastq > data1_aln.sam
Thanks
biobee
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