Dear Dr Tim,
I am trying to use LIGR seq analysis to find out chimeric reads in cyanobacterial species. In this regard, I am unable to install packages for Julia v0.4 REPL as suggested in the README document.
julia> map(Pkg.add, pkgs)
INFO: Initializing package repository /home/jssprakash/.julia/v0.4
INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl
fatal: unable to connect to github.com:
github.com[0: 20.207.73.82]: errno=Connection refused
ERROR: failed process: Process(git clone -q -b metadata-v2 git://github.com/JuliaLang/METADATA.jl METADATA, ProcessExited(128)) [128]
in run at ./process.jl:531
in anonymous at pkg/dir.jl:52
in cd at ./file.jl:22
in init at pkg/dir.jl:50
in cd at pkg/dir.jl:28
in add at pkg.jl:23
in map at tuple.jl:63
I have downloaded the recent version but it is not comptible with aligater suit. Importantly, while running aligater -h, it is showing aligater command not found.
detect : detect chimeric reads by recursive chaining of transcriptome SAM blocks
post : post-process LIG format files with BLAST or RACTIP
reclass : create 2D k-mer db and reclassify chimeras using heirarchical type
stats : compare crosslinked to mock-treated samples using multinomial statistics
table : compile interaction results into tabular format
at ./aligater line 80.
(base) jssprakash@jssprakash-ProLiant-ML350-Gen9:~/Aligater$ aligater -h
aligater: command not found
I am new to Julia. I am unable to run the aligater suit. I will be really obliged if you could help me with the doubts. I have separately generated the sam file by running bowtie with the parameters mentioned in the paper and my reference genome is a modified one separately generated by adding the non-conding RNA details that are not available in public databases. Now I need to detect the parameters using -detect and generate the table finally to get the chimeric reads.
Dear Dr Tim, I am trying to use LIGR seq analysis to find out chimeric reads in cyanobacterial species. In this regard, I am unable to install packages for Julia v0.4 REPL as suggested in the README document.
julia> pkgs ("ArgParse","Match","Distributions","GZip")
julia> map(Pkg.add, pkgs) INFO: Initializing package repository /home/jssprakash/.julia/v0.4 INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl fatal: unable to connect to github.com: github.com[0: 20.207.73.82]: errno=Connection refused
ERROR: failed process: Process(
git clone -q -b metadata-v2 git://github.com/JuliaLang/METADATA.jl METADATA, ProcessExited(128)) [128] in run at ./process.jl:531 in anonymous at pkg/dir.jl:52 in cd at ./file.jl:22 in init at pkg/dir.jl:50 in cd at pkg/dir.jl:28 in add at pkg.jl:23 in map at tuple.jl:63I have downloaded the recent version but it is not comptible with aligater suit. Importantly, while running aligater -h, it is showing aligater command not found.
(base) jssprakash@jssprakash-ProLiant-ML350-Gen9:~/Aligater$ ./aligater Usage: aligater [sub-command] [-h]
I am new to Julia. I am unable to run the aligater suit. I will be really obliged if you could help me with the doubts. I have separately generated the sam file by running bowtie with the parameters mentioned in the paper and my reference genome is a modified one separately generated by adding the non-conding RNA details that are not available in public databases. Now I need to detect the parameters using -detect and generate the table finally to get the chimeric reads.