Hi all,
I'm running into something strange.
I'm trying to do paired-end alignment with BWA.
I did the following:
bwa aln fasta pair1.fastq > pair1.sai
bwa aln fasta pair2.fastq > pair2.sai
Then, I did
bwa sampe fasta pair1.sai pair2.sai pair1.fasta pair2.fastq > bam
However, when I looked at my bam, I got alignments such as this:
seq1 117 chr10 49643024 0 * = 49643024 0 CCCGTATAACTCCATTCTTGGTTCTCTCCTCCAAGTCCATAACTTCCTTATATATCAATTCTTTCCACT
seq1 153 chr10 49643024 37 100M = 49643024 0 AGACAGCAGTCTAGAAGCAGCAGCTGGGCCTCTGGGCTGCTGTAGATGACTACTTGGGCCATCGGGGGG
My question is: shouldn't seq1 (first in pair; flag 117) have a "*" under column 3, signifying that it's unaligned?
What is going on here?
I'm running into something strange.
I'm trying to do paired-end alignment with BWA.
I did the following:
bwa aln fasta pair1.fastq > pair1.sai
bwa aln fasta pair2.fastq > pair2.sai
Then, I did
bwa sampe fasta pair1.sai pair2.sai pair1.fasta pair2.fastq > bam
However, when I looked at my bam, I got alignments such as this:
seq1 117 chr10 49643024 0 * = 49643024 0 CCCGTATAACTCCATTCTTGGTTCTCTCCTCCAAGTCCATAACTTCCTTATATATCAATTCTTTCCACT
seq1 153 chr10 49643024 37 100M = 49643024 0 AGACAGCAGTCTAGAAGCAGCAGCTGGGCCTCTGGGCTGCTGTAGATGACTACTTGGGCCATCGGGGGG
My question is: shouldn't seq1 (first in pair; flag 117) have a "*" under column 3, signifying that it's unaligned?
What is going on here?
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