I have illumina paired-end multiple-lane_reads of same individual which are distributed in 3 lanes like below;
C09FNACXX_EGLOB-140092_GTCAGT_L008_R1_001.fastq
C09FNACXX_EGLOB-140092_GTCAGT_L008_R1_002.fastq
C09FNACXX_EGLOB-140092_GTCAGT_L008_R2_001.fastq
C09FNACXX_EGLOB-140092_GTCAGT_L008_R2_002.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L001_R1_001.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L001_R1_002.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L001_R2_001.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L001_R2_002.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L002_R1_001.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L002_R1_002.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L002_R2_001.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L002_R2_002.fastq
They are all representing one individual (140092).
I am mapping these with BWA.
Question:
Are R1_001 and R2_001 in each lane the read-pairs?
if yes, I will probably able to do the aln command as following:
bwa aln refrencegenome.fa C09FNACXX_EGLOB-140092_ATATGA_L008_R1_001.fastq > aln_L008_1_1.sai
bwa aln refrencegenome.fa C09FNACXX_EGLOB-140092_ATATGA_L008_R1_002.fastq > aln_L008_1_2.sai
bwa aln refrencegenome.fa C09FNACXX_EGLOB-140092_ATATGA_L008_R2_001.fastq > aln_L008_2_1.sai
bwa aln refrencegenome.fa C09FNACXX_EGLOB-140092_ATATGA_L008_R2_002.fastq > aln_L008_2_2.sai
.
..
...
if yes, then how can I merge them in bwa sampe?
the original command is: bwa sampe ref.fa aln1.sai aln2.sai R1.fq R.fq > aln.sam
Here I have a confusion, actually I don't have aln1.sai aln2.sai R1.fq R2.fq but instead I will have;
aln1_1.sai aln1_2.sai aln2_1.sai aln2_2.sai for each lane.
So how I can merge all the many *.sai files into a single final_aln.sam?
My be I should consider R1_001 and R2_001 as paired reads and do the bwa sampe command as following;
bwa sampe ref.fa aln_L008_1_1.sai aln_L008_2_1.sai L008_R1_001.fastq L008_R2_001.fastq > aln_L008_1.sam
bwa sampe ref.fa aln_L008_1_2.sai aln_L008_2_2.sai L008_R1_002.fastq L008_R2_002.fastq > aln_L008_2.sam
.
..
..
and convert them to BAM files
and then merge them with samtools like;
samtools merge final.bam aln_L008_1.bam aln_L008_2.bam aln_L001_1.bam aln_L001_2.bam aln_L002_1.bam aln_L002_2.bam
I hope the question is clear.
I will be thankful to anyone who could help me with this question.
Cheers, Hossein.
C09FNACXX_EGLOB-140092_GTCAGT_L008_R1_001.fastq
C09FNACXX_EGLOB-140092_GTCAGT_L008_R1_002.fastq
C09FNACXX_EGLOB-140092_GTCAGT_L008_R2_001.fastq
C09FNACXX_EGLOB-140092_GTCAGT_L008_R2_002.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L001_R1_001.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L001_R1_002.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L001_R2_001.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L001_R2_002.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L002_R1_001.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L002_R1_002.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L002_R2_001.fastq
D0H2WACXX_EGLOB-140092_GTCAGT_L002_R2_002.fastq
They are all representing one individual (140092).
I am mapping these with BWA.
Question:
Are R1_001 and R2_001 in each lane the read-pairs?
if yes, I will probably able to do the aln command as following:
bwa aln refrencegenome.fa C09FNACXX_EGLOB-140092_ATATGA_L008_R1_001.fastq > aln_L008_1_1.sai
bwa aln refrencegenome.fa C09FNACXX_EGLOB-140092_ATATGA_L008_R1_002.fastq > aln_L008_1_2.sai
bwa aln refrencegenome.fa C09FNACXX_EGLOB-140092_ATATGA_L008_R2_001.fastq > aln_L008_2_1.sai
bwa aln refrencegenome.fa C09FNACXX_EGLOB-140092_ATATGA_L008_R2_002.fastq > aln_L008_2_2.sai
.
..
...
if yes, then how can I merge them in bwa sampe?
the original command is: bwa sampe ref.fa aln1.sai aln2.sai R1.fq R.fq > aln.sam
Here I have a confusion, actually I don't have aln1.sai aln2.sai R1.fq R2.fq but instead I will have;
aln1_1.sai aln1_2.sai aln2_1.sai aln2_2.sai for each lane.
So how I can merge all the many *.sai files into a single final_aln.sam?
My be I should consider R1_001 and R2_001 as paired reads and do the bwa sampe command as following;
bwa sampe ref.fa aln_L008_1_1.sai aln_L008_2_1.sai L008_R1_001.fastq L008_R2_001.fastq > aln_L008_1.sam
bwa sampe ref.fa aln_L008_1_2.sai aln_L008_2_2.sai L008_R1_002.fastq L008_R2_002.fastq > aln_L008_2.sam
.
..
..
and convert them to BAM files
and then merge them with samtools like;
samtools merge final.bam aln_L008_1.bam aln_L008_2.bam aln_L001_1.bam aln_L001_2.bam aln_L002_1.bam aln_L002_2.bam
I hope the question is clear.
I will be thankful to anyone who could help me with this question.
Cheers, Hossein.
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