can't find the genome nib files after installing crispr-do locally

[WANG Zifeng]

Hi, everyone,

     CRISPR-DO is the best sgRNA design tools.  Howevere, online tool the http://cistrome.org/crispr/tool is very slow.  

      I tried to install crisprdo locally on ubuntu16.04 following the instruction http://cistrome.org/crispr/source

      After installation, i encontered the problem:

bio817@bio817:~$ sudo crispr-do -g hg19 -c 11 --start=1285294 --end=1287328 --job-id=test --annotation ~/bio817/001_Work/000_index/021_crispr-do_hg19_exon/DHS_hg19.hammock ~/bio817/001_Work/000_index/021_crispr-do_hg19_exon/hg19.exon ~/bio817/001_Work/000_index/021_crispr-do_hg19_exon/hg19snp.sort

[2019-04-24 09:46:34] INFO    - Crispr-do script start.

[2019-04-24 09:46:34] INFO    - Workdir: test

[2019-04-24 09:46:34] INFO    - Job_id: test

[2019-04-24 09:46:34] WARNING - Workdir test is not empty.

Traceback (most recent call last):

  File "/usr/local/bin/crispr-do", line 119, in <module>

    core.design_sgrna(**opts.__dict__)

  File "/usr/local/lib/python2.7/dist-packages/crisprdo/core.py", line 745, in design_sgrna

    p.step_1_scan_PAM_on_region(outfile=resultfn)

  File "/usr/local/lib/python2.7/dist-packages/crisprdo/core.py", line 214, in step_1_scan_PAM_on_region

    twobit = TwoBitFile(open(STATIC_GENOME_2BIT.format(genome=genome, chrom=chrom), 'rb'))

IOError: [Errno 2] No such file or directory: '/data4/CistromeAP/static_libraries/assembly/hg19/rawgenome/hg19.2bit'

I tried to download hg19.2bit file and directly assign -g hg19.2bit,  failed.

Anyone can help me?

[Jian Ma]

Hi,

Before install crispr-do, you need to copy https://bitbucket.org/jianma/crisprdo/src/default/crisprdo/settings.py.sample to settings.py and modified the path of these static data. In your case the variable is STATIC_GENOME_2BIT.

The commandline crisprdo will not accelerate calculation, I suggest you try hg38 online

WANG Zifeng <zifen...@gmail.com> 于2019年4月24日周三 上午9:50写道：

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best，

Jian Ma,