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pritykinlab / guidescan-cli

A gRNA database generation tool.
http://www.guidescan.com
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gRNA design #31

Open AIqbal94 opened 3 weeks ago

AIqbal94 commented 3 weeks ago

Hi guys

I have been trying to use the guidescan command line interface to basically run the gRNA Design tool from the website but I am a bit confused on the protocol.

As a test run I gave the following coordinates to the web interface (using hg38);

chr1:6526905-6528918
chr1:6529247-6531892

and was able to get the attached excel file as output.

But I don't know how to get the same output using the command line tool.

So far I tried the generate_kmers.py and then used that output as input for the guidescan enumerate subcommand but the output looks like below

id,sequence,match_chrm,match_position,match_strand,match_distance,match_sequence,rna_bulges,dna_bulges,specificity
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr1,6528243,+,0,TCTGAGTGACGGGAAGTGCCAGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr6,53005777,-,3,TCTGAGTGACGtGgAGTcCCTGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr6,25230610,-,3,TCTGAGTGACaGcAAGTGCgTGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr12,113272832,-,3,TCTGAGTGAtGGGAAcTcCCAGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr2,120598929,-,3,TCTGAGTGAgGGGAAaTGgCAGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr11,79428624,-,3,TCTGAGTGctGGGAAaTGCCTGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr12,59157629,-,3,TCaGAcTGAaGGGAAGTGCCAGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr15,66750842,-,3,cCTGAGTGctGGGAAGTGCCAGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr10,116732790,+,3,TCTGAGTGACcGGgAGTGgCTGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr3,124525447,+,3,TCTGAGTaAaGGGAAGTaCCAGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr16,2969052,+,3,TCTGAGgGACGcGAgGTGCCAGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr8,40380728,+,3,TgTGAGTGAtGGGAAGaGCCAGG,0,0,0.231066
chr1:6526905-6528918:1338:+,TCTGAGTGACGGGAAGTGCCNGG,chr6,168272553,+,3,cCTGAtTGACaGGAAGTGCCGGG,0,0,0.231066
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chr1,6528445,+,0,GGGCTGAAAGTACCAAATGAAGG,0,0,0.212715
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chr13,30148092,-,1,GGGCTGAAAGTACCAAATcAAGG,0,0,0.212715
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chr18,36331607,+,2,GGGCTGAAgGTACCAAAgGAAGG,0,0,0.212715
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chr11,11511847,-,3,GGGCTGAAAGTcCCAgATcAGGG,0,0,0.212715
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chrX,151186473,-,3,GGGCTGAAAaTAtCAAATGtTGG,0,0,0.212715
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chr11,38815387,-,3,GGtagGAAAGTACCAAATGATGG,0,0,0.212715
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chr9,93933404,-,3,GtGCTGAAAGgACCAAAaGATGG,0,0,0.212715
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chr16,68810177,-,3,GaGCTGAAAGaACCAAgTGAGGG,0,0,0.212715
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chr4,72252384,-,3,tGGCTGAcAGTcCCAAATGATGG,0,0,0.212715
chr1:6526905-6528918:1540:+,GGGCTGAAAGTACCAAATGANGG,chr5,174117810,-,3,aGGCTGAAAGTAtgAAATGAAGG,0,0,0.212715

I would appreciate

results.xlsx