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.
• 2,163 views
•
link
written
by
zaroteary •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to design ARM PCR primers for SNP detection?
written by Milad •
-
Strain specific primers from multifasta file
written by rob •
-
Validate PCR DNA primers against whole de novel genome
written by qwzhang0601
-
software for Insilico Pcr
written by moohit21 •
-
Pairwisely detecting primer secondary structure: too many groups
written by bill-zt •
-
Poor PCR product
written by loly.pearl86 •
-
in silico PCR of designed primers against an assembled transcriptome
written by ahmad.iut
-
Bacterial identification - PCR primers - unknown target
written by RAZLICAK •
-
Primer design for HLA locus.
written by gskbioinfo143 •
-
In Silico Pcr Assay
written by Lee Katz
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...