Hi
I want to map the output of 4 separate illumina smrt cells against a pacbio reference genome using BWA. I've indexed the full genome.
I can try run the the equivalent of this line, but using additional reads:
bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
However, if I try
bwa mem ref.fa read1.fq read2.fq read3.fq read4.fq > aln-pe.sam
include read3.fq or more nothing runs.. Instead I get the usage instructions for bwa.
Is there a way to map 4 illumina runs against the reference genome at once, or am I misunderstanding this process?
There are simply 4 runs to increase robustness.
2 answers
Your first command lined is for paired end sequencing. Is that what you have?
If you do not have paired end sequencing, just two fastqs of the same single-end library, then your first command line is wrong.
If you have 4 fastqs that are all the same single end library, you can cat them all together before giving them to bwa
cat read*.fq | bwa mem ref.fa - > out.sam
Hi There are some posts similar to yours. Have a look.
bwa for multiple fastq files , BWA mem on multiple samples, perl script for BWA-mem on multiple different files
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It is unclear what you do. Do you have different paired-end samples, all with R1 and R2? Should all the four samples go to the same SAM file or to different ones?
These are 4 separate runs of illumina output that I am supposed to analyse and compare to my pacbio genome that I sequenced. I want all 4 in the same SAM file.
You are mixing terminologies here. PacBio sequencer uses SMRTCells where as Illumina sequencers use flowcells. Do you have 4 separate samples/lanes/flowcells worth Illumina data? Depending on the answer there would be a different solution.
Thanks for correcting me. I was getting confused and using the wrong terminology. It is from flow cells. I've been asked to map illumina short reads against my pacbio genome assembly to examine the coverage.