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# Cas13gRNA Park
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1. Reference
Montero et al., Genome-scale pan-cancer interrogation of lncRNA dependencies using CasRx. Nat Methods. 2024 Apr;21(4):584-596.
https://pubmed.ncbi.nlm.nih.gov/38409225/

2. GitHub
https://github.com/roland-rad-lab/Genome-scale-pan-cancer-interrogation-of-lncRNA-dependencies-using-CasRx/tree/main/gRNA_design

3. How to use
3-1. Access to https://gmsuite.hgc.jp/crRNA/index.php
3-2. Enter the user account and passwd
3-3. (1) Upload a text input file (*** make sure the file format and input type)
3-4. (2) Specify the parameter set
3-5. (3) Specify your email address
3-6. Click the submit button
3-7. Check emails from the system

4. Download the result TAR file that is notified in an email from the system.
   The TAR file will be deleted after 10 days.

5. Decompress the TAR file using "tar xfz tarFilename"
NOTE: if the TAR file included "crRNA.lock", it means that this run has been failed (e.g. memory).

5-1. An example of succeeded case (input type=1)

sFLNRvqt6W (directory name: token by random letters)
|-- README.txt (this file)
|-- crRNA.age  (shell script submitted to a batch system)
|-- crRNA.conf (parameters)
|-- crRNA_sFLNRvqt6W.o108709764 (output from the batch system)
|-- input_example1.txt (the input file user uploaded)
`-- result (directory)
    |-- prediction (preliminary gRNAs prediction for each listed in the input file)
    |   |-- ENST00000380152_CasRxguides.csv
    |   |-- ENST00000380152_CasRxguides.fa
    |   |-- ENST00000380152_CasRxguides.pdf
    |   |-- ENST00000614259_CasRxguides.csv
    |   |-- ENST00000614259_CasRxguides.fa
    |   |-- ENST00000614259_CasRxguides.pdf
    |   `-- input_sequence.fa (DNA sequences for each listed in the input file)
    |-- prediction.csv
    `-- prediction_filtered
        |-- ENST00000380152_CasRxguides_bowtie2.sam
        |-- ENST00000380152_CasRxguides_filtered.csv (final gRNAs)
        |-- ENST00000614259_CasRxguides_bowtie2.sam
        `-- ENST00000614259_CasRxguides_filtered.csv (final gRNAs)

5-2. An example of succeeded case (input type=3)

GDTICEW5iU
|-- README.txt
|-- crRNA.age
|-- crRNA.conf
|-- crRNA_GDTICEW5iU.o108709758
|-- input_example3.csv
`-- result
    |-- prediction
    |   |-- human_lncrna_fused_174_CasRxguides.csv
    |   |-- human_lncrna_fused_174_CasRxguides.fa
    |   |-- human_lncrna_fused_174_CasRxguides.pdf (a plot for distri. quantiles)
    |   |-- human_lncrna_fused_205_CasRxguides.csv
    |   |-- human_lncrna_fused_205_CasRxguides.fa
    |   |-- human_lncrna_fused_205_CasRxguides.pdf
    |   `-- input_sequence.fa
    |-- prediction.csv
    `-- prediction_filtered
        |-- human_lncrna_fused_174_CasRxguides_bowtie2.sam
        |-- human_lncrna_fused_174_CasRxguides_filtered.csv
        |-- human_lncrna_fused_205_CasRxguides_bowtie2.sam
        `-- human_lncrna_fused_205_CasRxguides_filtered.csv


5-3. An example of FAILED case (input type=2)

sD2REfgb5O
|-- README.txt
|-- crRNA.age
|-- crRNA.conf
|-- crRNA_sD2REfgb5O.o108710033
|-- input_example2.csv
|-- prazci.fa
|-- prazci_dp.ps
|-- prazci_lunp
|-- result
|   |-- prediction
|   |   |-- Target1_CasRxguides.csv
|   |   |-- Target1_CasRxguides.fa
|   |   |-- Target1_CasRxguides.pdf
|   |   |-- Target2_CasRxguides.csv
|   |   |-- Target2_CasRxguides.fa
|   |   |-- Target2_CasRxguides.pdf
|   |   `-- input_sequence.fa
|   |-- prediction.csv
|   `-- prediction_filtered
|       |-- *_bowtie2.sam
|       |-- *_filtered.csv
|       |-- Target1_CasRxguides_bowtie2.sam
|       |-- Target1_CasRxguides_filtered.csv
|       |-- Target2_CasRxguides_bowtie2.sam
|       `-- Target2_CasRxguides_filtered.csv
|-- sxlcmj.fa
|-- sxlcmj_dp.ps
`-- sxlcmj_lunp