I was using TEQC to do quality control of my WES bam files aligned by bwa-mem.
My data are paired end, so a function reads2pairs is called to make the paired-end reads to be a single fragment.
I then get this error:
> readpairs <- reads2pairs(reads)
Error in reads2pairs(reads) : read pair IDs do not seem to be uniqueI asked in the bioconductor support site and went to the source code of that function.
rm command is very dangerous because after you remove something, you can not recover it. There is no trash bin in the unix system.
If you have some raw data (e.g fastq files), you'd better make them safe by changing the file permissions.
in an empty directory, make a folder foo:
mkdir test
cd test
mkdir foo
cd foo
touch {1..4}.fastqs
see https://gist.github.com/ckandoth/c16b9a423b54dc0a7a37 for installing perl5.22 locally
If you want to install modules for users without root. https://stackoverflow.com/questions/2980297/how-can-i-use-cpan-as-a-non-root-user
wget -O- http://cpanmin.us | perl - -l ~/perl5 App::cpanminus local::lib
eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`
echo 'eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`' >> ~/.profile
echo 'export MANPATH=$HOME/perl5/man:$MANPATH' >> ~/.profile
I use sshfs to mount remote servers.
but I also want to connecting windows servers to my ubuntu.
If there's one good thing that I can say about Windows XP is that it supports the SMB protocol. This enables a computer running Windows to share files, folders, and more with another PC. All that other PC needs is the right software to take advantage of the SMB protocol. Luckily, that software is available for GNU/Linux.
on mac, I can click the Finder bar --->Go---> Connect to Server and then type in the address.
cores, cpus and threads :
http://www.slac.stanford.edu/comp/unix/package/lsf/currdoc/lsf_admin/index.htm?lim_core_detection.html~main
Traditionally, the value of ncpus has been equal to the number of physical CPUs. However, many CPUs consist of multiple cores and threads, so the traditional 1:1 mapping is no longer useful. A more useful approach is to set ncpus to equal one of the following:
The latest version of vep is on github http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer
it is version 89 when this gist was written.(bioinformatics tools evolve too fast!)
check this gist as well https://gist.github.com/ckandoth/f265ea7c59a880e28b1e533a6e935697
From Mike Love:https://gist.github.com/mikelove/f539631f9e187a8931d34779436a1c01
An R implementation of the rule:
Archive generated fastq files are organised by run accession number under vol1/fastq directory in ftp.sra.ebi.ac.uk:
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/[/]/
is the first 6 letters and numbers of the run accession ( e.g. ERR000 for ERR000916 ),
## DEseq2 built-in function
plotPCA(vsd.fast, intgroup=c("subtype"))
##SVD to get PCs mannually
X<- assay(vsd.fast)
## center X
X<- t(scale(t(X),center=TRUE,scale=FALSE))
| # This code will get all clinical indexed data from TCGA | |
| library(TCGAbiolinks) | |
| library(data.table) | |
| clinical <- TCGAbiolinks:::getGDCprojects()$project_id %>% | |
| regexPipes::grep("TCGA",value=T) %>% | |
| sort %>% | |
| plyr::alply(1,GDCquery_clinic, .progress = "text") %>% | |
| rbindlist | |
| readr::write_csv(clinical,path = paste0("all_clin_indexed.csv")) |
This is the default behavior for SSH. It protects user keys by enforcing rwx------ on $HOME/.ssh and ensuring only the owner has write permissions to $HOME. If a user other than the respective owner has write permission on the $HOME directory, they could maliciously modify the permissions on $HOME/.ssh, potentially hijacking the user keys, known_hosts, or something similar. In summary, the following permissions on $HOME will be sufficient for SSH to work.
- rwx------
- rwxr-x---
- rwxr-xr-x
>SSH will not work correctly and will send warnings to the log facilities if any variation of g+w or o+w exists on the $HOME directory.