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Old 06-28-2011, 02:52 AM   #1
mixter
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Location: Munich, Germany

Join Date: May 2010
Posts: 22
Smile Fasta with one entry per chromosome (for methylation analysis and others)

Hello,

I'm currently evaluating different tools for methylation analysis of HTS data (bisulfite, RRBS). I already know and use Bismark, but I'd prefer to also handle data directly in R/bioconductor, in order to reuse analyses from existing packages where possible.

I noticed that many packages and tools for methylation analysis require FASTA files of aligned sequences. This alone is not a problem (SAM can easily be convered to FASTA using awk, perl or fastx tools).

However, all tools I've seen so far do not handle multiple FASTA files well, most of them not at all. The expected input for most packages (e.g. methVisual bioconductor package) are FASTA files with a single sequence, e.g. one entry per chromosome.

So, can anyone here recommend a good way of converting SAM or FASTA with one entry per aligned read to FASTA with one entry per chromosome?

This is basically conversion from aligned short reads to reference genome (refSeq) format, so I guess there should be a standard way to do it, but I couldn't find one yet. Thanks in advance
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