Find_SNPs

[mark carlile]

Hello,
I'm hoping to use the Find_SNP scripts on some mouse RNAseq data in the very near future.  After looking at the README information it looks like I need to call:

Retrieve_SNP_Positions.sh [reference] [output_dir] [sample1.bam] [sample2.bam]
Questions:
What is the [reference] file? Is it just a representative genome (muse in my case)?  In what format should this file be used (.fa, .fna, ...)
How much computing power is required for running this against deep RNASeq data (.bam files)?

Many thanks in advance

Mark

[Martin Asser Hansen]

There seems to be some misunderstanding here. Biopieces do have the facility to locate SNPs using the Biopiece find_SNPs:

https://code.google.com/p/biopieces/wiki/HowTo#Finding_SNPs_and_DIPs

However, that is not the same tools as the Find_SNP you are mentioning - I have no knowledge of that one.

Cheers,

Martin

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[mark carlile]

Sorry - My mistake - got myself confused after lots of searching the web.

I'll have a look at the link you sent and have a go at using the scripts.  I might be posting again soon (?)
Many thanks

Mark