Daniel:Notebook/HiResChrPaint/2014-6-19

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Revision as of 18:06, 19 June 2014 by >Djacobse (→‎Probe Mining)
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Probe Design (Started 06/17/2014)

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Probe Mining

The OligoArray script might actually need the blast database broken up into 1kb chunks for some reason. So, let's try that.

  1. Create BLAST database from fragmented genome
    1. formatdb -i in_hg38.fas -p T -o F
[formatdb] WARNING: Cannot add sequence number 1953021 (lcl|range=hg38:1953020000-1953020999) because it has zero-length.
[formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.

So that's a fatal error.

The instructions call for concatenating all the fasta files into one. I did this step using cat, but they suggest using their java script, so I'll try that.

  1. Concatenate fasta files
    1. java ConcatenateFiles hg38_cat.fas *.fa
  2. Fragment genome into pieces
    1. python ../bin/input_blocks.py
    2. Please enter the filename, "chr2R_sorted_oligo.txt" or "chr2R_intersect.bed" etc.: hg38_cat.fas