Daniel:Notebook/HiResChrPaint/2014-1-30

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Predicting FISH Signals[edit]

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From yesterday's results, I would say that I'm still unsure what kind of signal I should be looking for. In an effort to improve my knowledge, I'm going to align the probe sets to the genome, and predict how many spots I should be seeing. According to Cremer and Cremer (2010), there are distinct chromosome territories:

File:Chromosome Territories.png

Based on this, I can predict how many dots and what kind of concentration I should see them at within the nucleus. My suspicion is that there are far too many in the V6S3 set right now, and that the signal seen there is just noise, or at least not specific enough to accurately call.

Aligning the signals[edit]

Generate Novoalign Genome

novoindex genome_hg19.nix genome.fa

Align probe sequences to Genome

novoalign -d haplotyping/genome_hg19.nix -f V6S3_probeseq.fastq -o SAM > V6S3_alignment.sam &