Open xucaoling opened 1 year ago
Hi xucaoling, I'll get these disappearing files fixed soon, please try git clone and run again then.
fixed already.
Thanks @liumz93
The script 'TranslocPlot.R' calls
source_local("Rsub.R")
source_local("TranslocHelper.R")
Do you have those files as well?
Sorry for the problems, I have provided explanatory notes in README.md, Thanks!
Dear liumz, Thank you very much for your scripts, when i use define_statistics_add_filter.py, it shows:
See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy close_inver.drop(columns=['Microhomolog_len'], inplace=True) Error in file(file, "rt") : Calls: getCytoBands -> read.delim -> read.table -> file Warning message: In file(file, "rt") : can't open '/D1/DB/Genome/Human/bwa_indexes/GRCh38/annotation/cytoBand.txt': There is no file or directory for that Stop execution Can't locate PerlSub.pl in @INC (@INC contains: /D1/Bio/CRISPR/PemSeq/lib /root/perl5/lib/perl5/x86_64-linux-thread-multi /root/perl5/lib/perl5 /D1/APP/Script/Anaconda/lib/site_perl/5.34.0/x86_64-linux-thread-multi /D1/APP/Script/Anaconda/lib/site_perl/5.34.0 /D1/APP/Script/Anaconda/lib/5.34.0/x86_64-linux-thread-multi /D1/APP/Script/Anaconda/lib/5.34.0 .) at /D1/Bio/CRISPR/PemSeq/tools/TranslocHTMLReads_PEMQ.pl line 21.
But i do not find cytoBand.txt, refGene.bed and PerlSub.pl, Could you share it?
Hi YanpinHu,
Now you can find the PerlSub.pl in the tool folder. As for cytoBand.txt, refGene.bed, you can download them from UCSC genome browser. For hg38: https://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/
Thanks,
Thanks! The code is running properly.
Dear liumz, Thank you very much for your scripts, when i use define_statistics_add_filter.py, it shows: