beginner question BWA program

Question

[reza]

hi

i want to map my own reads (illumina hiseq) to reference using "bwa mem". i have 2 lane of paired end data (read1.fastq, read2.fastq, read11.fastq and read22.fastq). in bwa tutorial, command for map to reference of paired end reads is "bwa mem ref.fa read1.fq read2.fq > aln-pe.sam". now i have 4 read files for mapping to reference, what is command for my reads?

"bwa mem ref.fa read1.fq read2.fq read11.fq read22.fq> aln-pe.sam" is true?

Answer 1

[Pierre Lindenbaum]

your choice is:

1) merge the forward and the reverse fastq files

cat read1.fq read11.fq > R1.fq
cat read2.fq read22.fq > R2.fq
bwa mem ref.fa R1.fq R2.fq> aln-pe.sam

or

bwa mem ref.fa <(cat read1.fq read11.fq ) <( cat read2.fq read22.fq ) > aln-pe.sam

2) align both pairs

bwa mem ref.fa R1.fq R2.fq | samtools sort -T tmp -O bam -o f1.bam -
bwa mem ref.fa R11.fq R22.fq | samtools sort -T tmp -O bam -o f2.bam -

and then merge the sorted pairs.

samtools merge merged.bam f1.bam f2.bam

[WouterDeCoster]

-O is unnecessary when -o is specified because the extension will be used to determine the out-type.

[reza]

thanks a lot Pierre, your answer is complete

[WouterDeCoster]

If he answered your question, then accept his answer as the solution.

Answer 2

[reza]

hi again dear Pierre

After mapping to reference using "bwa mem", downstream analysis in my project are variant calling using samtools and CNV detection using CNV-seq. In your opinion, default setting in bwa is proper for my goal? i must use -M in "bwa mem" (after mapping i want to mark duplicates via Picard) ?

thanks in advance for your kindly helps