Daniel:Notebook/HiResChrPaint/2014-6-19: Difference between revisions
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>Djacobse |
>Djacobse |
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#Fragment genome into pieces | #Fragment genome into pieces | ||
##python ../bin/input_blocks.py | ##python ../bin/input_blocks.py | ||
## | ##''Please enter the filename, "chr2R_sorted_oligo.txt" or "chr2R_intersect.bed" etc.:'' hg38_cat.fas |
Revision as of 18:06, 19 June 2014
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