Hi,
I used bwa to map a pair-end SOLiD data. samtools flagstat showed 66% mapped reads, but only 0.17% properlly mapped.
Here are some detail and my cmd lines:
my input file: SOLID_F3.csfasta + SOLID_F3_QV.qual
SOLID_R3.csfasta + SOLID_R3_QV.qual
(1) make color-space reference: bwa index -p hg18_cs.fa -a bwtsw -c hg18.fa
(2) convert solid to fastq: perl solid2fastq.pl SOLID_ test
this resulted test.read1.fastq.gz test.read2.fastq.gz test.single.fastq.gz
unzip them
(3) bwa aln -t 4 -c hg18_cs.fa test.read1.fastq > test_aln_sa1.sai
bwa aln -t 4 -c hg18_cs.fa test.read2.fastq > test_aln_sa2.sai
(4) bwa sampe hg18_cs.fa test_aln_sa1.sai test_aln_sa2.sai test.read1.fastq test.read2.fastq > aln.sam
(5) samtools view -bt hg18_cs.fa -o aln.bam aln.sam
[samopen] SAM header is present: 25 sequences.
(6) $ samtools flagstat aln.bam
The resutl shows mapped (66.64%), properly paired (0.15%)
Can anyone tell me where I did wrong?
Thanks!
I used bwa to map a pair-end SOLiD data. samtools flagstat showed 66% mapped reads, but only 0.17% properlly mapped.
Here are some detail and my cmd lines:
my input file: SOLID_F3.csfasta + SOLID_F3_QV.qual
SOLID_R3.csfasta + SOLID_R3_QV.qual
(1) make color-space reference: bwa index -p hg18_cs.fa -a bwtsw -c hg18.fa
(2) convert solid to fastq: perl solid2fastq.pl SOLID_ test
this resulted test.read1.fastq.gz test.read2.fastq.gz test.single.fastq.gz
unzip them
(3) bwa aln -t 4 -c hg18_cs.fa test.read1.fastq > test_aln_sa1.sai
bwa aln -t 4 -c hg18_cs.fa test.read2.fastq > test_aln_sa2.sai
(4) bwa sampe hg18_cs.fa test_aln_sa1.sai test_aln_sa2.sai test.read1.fastq test.read2.fastq > aln.sam
(5) samtools view -bt hg18_cs.fa -o aln.bam aln.sam
[samopen] SAM header is present: 25 sequences.
(6) $ samtools flagstat aln.bam
The resutl shows mapped (66.64%), properly paired (0.15%)
Can anyone tell me where I did wrong?
Thanks!
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