Daniel:Notebook/HiResChrPaint/2014-6-19
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Probe Design (Started 06/17/2014)
Probe Mining
The OligoArray script might actually need the blast database broken up into 1kb chunks for some reason. So, let's try that.
- Create BLAST database from fragmented genome
- 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.
- Concatenate fasta files
- java ConcatenateFiles hg38_cat.fas *.fa
- Fragment genome into pieces
- python ../bin/input_blocks.py
- Please enter the filename, "chr2R_sorted_oligo.txt" or "chr2R_intersect.bed" etc.: hg38_cat.fas
- Please enter the chromosome or assembly, "chr1 or ch2R, etc.: hg38
Killed
Couldn't have said it better myself.
Trying again using the Wu lab version of the fasta file. This is an older version (hg19/gr37, not gr38), but it'll have to do.
- Format BLAST database
- formatdb -i hg19.fas -p T -o F