In silico PCR with BAM files?

Question

[zaroteary]

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.

[rozanskide]

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).

[zaroteary]

After I converted my BAM file to FASTA, the sequences are all in fragments of ~100 bp with overlaps. Example:

HS1:369:C3W70ACXX:8:1312:17711:59403/2 TAAACCCTAAACCCTAAACCCTAAACCCTCTCAAATCTGGTCATCATTTTTGACCGGATATTAGGTTTCATAAAACTGTAAAGTTACATACCTGTCAAAT HS1:369:C3W70ACXX:8:2113:18337:16744/2 AACCCTAAACCCTAAACCCTCTCAAATCTGGTCATCATTTTTGACCGGATATTAGGTTTCATAAAACTGTAAAGTTACATACCTGTCAAATCCGATCAAT HS1:369:C3W70ACXX:8:2111:18597:56001/1 GATTGATCGGATTTGACAGGTATGTAACTTTACAGTTTTATGAAACCTAATATCCGGTCAAAAATGATGACCAGATTTGAGAGGGTTTAGGGTTTAGGGT

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...