CHOPCHOP command line

Question

[gernophil]

Hey everyone, is anyone using the CLI version of CHOPCHOP for sgRNA design? I am trying to get it to work, but I have some questions about it.

1. I need a .gene_table file that I can extract from the UCSC. However, the tracks RefSeq Genes or Ensemble Genes are not available. for RefSeq Genes NCBI RefSeq seems to be the correct track. However, I can't find an proper Ensemble Genes track here. Any ideas where to find this?

2. Is there a way to directly use HGNC Symbols as IDs for the query?

3. Do all reference files (.2bit, .ebwt, .gene_table) need to be in different folders?

Answer 1

[regis90]

This is described in README.

1. ":gene_table" is simple genePred table with named columns e.g. https://chopchop.cbu.uib.no/genomes/isoforms/hg38.gene_table You could transform gff&gtf into genePred by using tools like http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred

2. To use the symbols you have to have them in the proper column in the genePred table, you could process the table to replace the ensemble gene names, or something like this might work

   gtfToGenePred -genePredExt -geneNameAsName2 gencode.v29.annotation.gtf hg38.genePred
   

3. Paths to the reference files are specified in the config.json

{  
  "PATH": {  
    "PRIMER3": "./primer3_core",  
    "BOWTIE": "bowtie/bowtie",  
    "TWOBITTOFA": "./twoBitToFa",  
    "TWOBIT_INDEX_DIR": "/your/full/path/to/2bit_folder",  
    "BOWTIE_INDEX_DIR": "/your/full/path/to/ebwt_folder",  
    "ISOFORMS_INDEX_DIR": "/your/full/path/to/ebwt_transcriptome_folder_and_2bit_of_genome",  
    "ISOFORMS_MT_DIR": "/your/full/path/to/vienna_MT_folder",  
    "GENE_TABLE_INDEX_DIR": "/your/full/path/to/genePred_folder"  
  },  
  "THREADS": 1  
}