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get_cuts_single_locus.sh missing #10

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hejing3283 opened this issue May 25, 2021 · 3 comments
Closed

get_cuts_single_locus.sh missing #10

hejing3283 opened this issue May 25, 2021 · 3 comments

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@hejing3283
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Hi,

I after running the example data, I got no error. But I cannot find the get_cuts_single_locus.sh file. Could you help?
@fl-yu
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fl-yu commented May 25, 2021

Thanks for your interest in our tool!
I will make an update this weekend for get_cuts_single_locus.sh

@fulviodan13
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Hi @fl-yu
get_cuts_single_locus.sh still missing.
Thank you

@fl-yu
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fl-yu commented Jul 23, 2021

Hey guys, sorry for the delayed reply. Excited to fix this missing function.
I have re-written the get_cuts_single_locus.sh, which is more convenient to use and allows to generate not only the single genomic locus cut profile but also those of whole genome-wide.

What I have changed (you need to update)

1. bulk-config.json file (the template for your configuration)
     "bdg2bwbin": "/gcdata/gcproj/fulong/Software/cutrun-test/CUT-RUNTools-2.0/install", 
2. newly added script 'get_cuts_single_locus.sh' in the folder /GitHub/CUT-RUNTools-2.0/src/bulk
3. newly added tool of 'bedGraphToBigWig' in the folder /GitHub/CUT-RUNTools-2.0/install

We need the configuration file (tell the code where the necessary software is), a processed BAM file of CUT&RUN/CUT&Tag, a region of interest (roi; in the format chr2:60457194-60553654), and an output directory"

Syntax: ./get_cuts_single_locus.sh configuration_file bam_file roi outputdir
options:
configrue_file     The configuration file, you may use one for running the bulk pipeline. Except for the software info, experiment type (cut&run or cut&tag) will be also used
bam_file               a processed BAM file from bulk pipeline
roi                    a region of interest (roi; in the format chr2:60457194-60553654). If you want to generate the whole genome profile instead of a particular genomic locus, please specify this parameter as 'whole_genome'
outputdir              The directory for output, e.g. /dir/for/output

Example usage:
      cd /Users/fyu/Documents/GitHub/CUT-RUNTools-2.0/src/bulk
      chmod +x ./get_cuts_single_locus.sh
      ./get_cuts_single_locus.sh scriptdir/bulk-config.json /cutruntools/mysample.bam chr2:60457194-60553654 /my/singlelocus/dir

Please let me know if you have any questions/issues on this.

@fl-yu fl-yu closed this as completed May 25, 2022
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@hejing3283 @fl-yu @fulviodan13