websites for regular expression test
http://www.txt2re.com/index-python.php3
https://regex101.com/
Sep 20, 2019
Sep 16, 2019
How to copy files from one machine to another using ssh [duplicate]
https://unix.stackexchange.com/questions/106480/how-to-copy-files-from-one-machine-to-another-using-ssh
Syntax:
scp <source> <destination>
To copy a file from B
to A
while logged into B
:scp /path/to/file username@a:/path/to/destination
To copy a file from B
to A
while logged into A
:scp username@b:/path/to/file /path/to/destination
IGV : tracks for normalize coverage Data (need igvtools to make .tdf files)
https://software.broadinstitute.org/software/igv/igvtools
https://software.broadinstitute.org/software/igv/igvtools_commandline
The igvtools utility provides a set of tools for pre-processing data files. File names must contain an accepted file extension, e.g. test-xyz.bam. Tools include:
igvtools count
Supported input file formats are: .sam, .bam, .aligned, .psl, .pslx, and .bed.
Usage:
igvtools count [options] [inputFile] [outputFile] [genome]
Select to normalize tracks containing coverage data in .tdf files that were created using igvtools. This normalization option multiplies each value by [1,000,000 / (totalReadCount)].
https://software.broadinstitute.org/software/igv/igvtools_commandline
The igvtools utility provides a set of tools for pre-processing data files. File names must contain an accepted file extension, e.g. test-xyz.bam. Tools include:
- toTDF
Converts a sorted data input file to a binary tiled data (.tdf) file.
Used to preprocess large datasets for improved IGV performance.
Supported input file formats: .cn, .gct, .igv, .res, .snp, and .wig
Note: This tool was previously known as tile
- count
Computes average alignment or feature density for over a specified window size across the genome and outputs a binary tiled data .tdf file, text .wig file, or both depending on inputs.
Used to create a track that can be displayed in IGV, for example as a bar chart.
Supported input file formats: .aligned, .bam, .bed, .psl, .pslx, and .sam
- index
Creates an index file for an ASCII alignment or feature file.
Index files are required for loading alignment files into IGV, and can significantly improve performance for large feature files. The file must be in sorted order by start position.
Supported input file formats: .aligned, .bed, .psl, .sam, .bam, and .vcf (v3.2)
- sort
Sorts the input file by start position.
Used to prepare data files for tools that required sorted input files.
Supported input file formats: .aligned, .bed, .cn, .igv, .psl, .sam, .bam, and .vcf
From IGV: igvtools is accessed by selecting Tools>Run igvtools.
igvtools count
Supported input file formats are: .sam, .bam, .aligned, .psl, .pslx, and .bed.Usage:
igvtools count [options] [inputFile] [outputFile] [genome]
The input file must be sorted by start position
http://software.broadinstitute.org/software/igv/book/export/html/6To load normalized coverage track to IGV
View -> Preferences -> Tracks
Select to normalize tracks containing coverage data in .tdf files that were created using igvtools. This normalization option multiplies each value by [1,000,000 / (totalReadCount)].
- This is only available for .tdf files created using igvtools builds dated 1/28/2010 or later. Earlier versions of igvtools did not record the total read count.
- This selection takes effect with new sessions loaded afterwards.
Installing CMake
https://cmake.org/install/
https://cmake.org/download/
https://gist.github.com/1duo/38af1abd68a2c7fe5087532ab968574e#file-centos-install-cmake-from-source-md
https://cmake.org/download/
https://gist.github.com/1duo/38af1abd68a2c7fe5087532ab968574e#file-centos-install-cmake-from-source-md
Compile from source and install
tar zxvf cmake-3.*
cd cmake-3.*
./bootstrap --prefix=/usr/local
make
make install
Validate installation
cmake --version
cmake version *.*.*
CMake suite maintained and supported by Kitware (kitware.com/cmake).
Install, uninstall RPM on linux (CentOS, RHEL, Fedora)
https://phoenixnap.com/kb/how-to-install-rpm-file-centos-linux
Install RPM on Linux
sudo rpm –i sample_file.rpm
sudo yum localinstall sample_file.rpm
Remove RPM Package
sudo rpm –e sample_file.rpm
Sep 4, 2019
Using grep -v on multiple arguments
https://www.thegeekstuff.com/2011/10/grep-or-and-not-operators
Using grep -v on multiple arguments
Using grep -v on multiple arguments
grep -v -e foo -e bar file
grep -Ev 'word1|word2'
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