In silico PCR with BAM files?
Dear all,
I have a .fa file for my organism and several .bam files for my isolates. I have designed some PCR primers for the isolates. Are there any programs that would allow me to run In silico PCR with the bam files?
Thank you.
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zaroteary •
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Hi zaroteary, Maybe you can convert your bam files to fasta - check BAM/SAM to FASTA conversion and then use in-silico PCR from UCSC ( download http://hgwdev.cse.ucsc.edu/~kent/exe/linux/isPcr.zip).
After I converted my BAM file to FASTA, the sequences are all in fragments of ~100 bp with overlaps. Example:
Do I need to reconstruct the genome before going into in-silico PCR? If so, how do I do it? Sorry, if this is a stupid question, I'm new to all these...