xTea | Comprehensive TE insertion identification with WGS/WES data | Genomics library
kandi X-RAY | xTea Summary
kandi X-RAY | xTea Summary
xTea (comprehensive transposable element analyzer) is designed to identify TE insertions from paired-end Illumina reads, barcode linked-reads, long reads (PacBio or Nanopore), or hybrid data from different sequencing platforms and takes whole-exome sequencing (WES) or whole-genome sequencing (WGS) data as input.
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Top functions reviewed by kandi - BETA
- Parse options
- Calls MEAS consensus
- Reassign reads with polyA
- Realign a polyA
- Realign reads to aligned BWA
- Parse a clip alignment file
- Return True if the sequence contains amino acids
- Calls candidate_transduction_v3
- Given a list of FASTQ file and a list of candidates collect all regions for each chromosome
- Collect all the clipped reads of the candidates
- Call the novel - Sink TD
- Calculate peak candidate sites
- Filter sites by multiple alignment
- Call TEI from multiple alignmts
- Performs a somatic EClipDiscFilter
- Calculate mean size for each read group
- Call TEI from multiple alignment files
- Checks the seprt dispersion of the SeeptDisc
- Run Gnrt shell
- Perform siblings based on existing alignment
- Parse DiscAlignAlignment file
- Extract reads by name in parallel
- Parse aligned clip alignment file
- Call mosaic from multiple samples
- Calculate the peak candidate sites using the standard deviation of the peak window
- Generate population VCF for population
xTea Key Features
xTea Examples and Code Snippets
Community Discussions
Trending Discussions on xTea
QUESTION
I wrote a small program which uses an XTEA cipher algorithm to encipher or decipher a given textfile. It all worked fine until I started to tidy up my program.
Here's the code that used to work:
...ANSWER
Answered 2021-Feb-26 at 00:41StoreCipherKey Function:
QUESTION
I have built the FFmpeg with libx264 into static libs, here is my directory tree.
...ANSWER
Answered 2021-Feb-22 at 07:15I made a mistake in the build script:
QUESTION
Imagine that following byte array contains all bytes of a executable file (.exe) (that on pratice this not is possible set inside source code because there are much bytes in this file type (.exe) and Visual Studio will crashe)
...ANSWER
Answered 2020-Oct-08 at 18:53You don't format at all, just write raw bytes. You are reading raw bytes using
QUESTION
I have an input byte array:
...ANSWER
Answered 2020-Apr-22 at 20:32Maybe someone will come in handy. The library “golang.org/x/crypto/xtea” does not include the XTEA algorithm with the ECB model because of its insecurity, therefore I wrote my own version:
QUESTION
I cannot understand how to build Botan for android, according on the instruction here:
$ export CXX=/opt/android-ndk/toolchains/llvm/prebuilt/linux-x86_64/bin/aarch64-linux-android28-clang++
$ ./configure.py --os=android --cc=clang --cpu=arm64
i cannot understand how to use this commands on Windows, also reading previous issues did not help me, can you tell me how did you build this library on windows step-by-step, just your command examples?
I used --cc-bin option of configure.py to specify the path to the compiler, it is considered a solution for windows, but what i have is:
...ANSWER
Answered 2020-Mar-21 at 22:13It seems Botan support for building Android binaries on Windows hosts is limited. You will have to use dark magic to make this work.
The build process consists of two phases, the configuration phase and the make phase.
The Android-specific instructions in the documentation you linked do not cover the whole build process, only the configuration phase. For the make phase, you then have to follow the Windows-specific instructions (link).
Configuration phase:You will need the following binaries, adjust the paths to your machine:
clang++ (note the
.cmdat the end):C:\Development\android-ndk-r19c-windows-x86_64\android-ndk-r19c\toolchains\llvm\prebuilt\windows-x86_64\bin\armv7a-linux-androideabi28-clang++.cmdar:
C:\Development\android-ndk-r19c-windows-x86_64\android-ndk-r19c\toolchains\llvm\prebuilt\windows-x86_64\bin\arm-linux-androideabi-ar.exe
In the Botan folder, run the configure command:
QUESTION
I am trying to decrypt Block TEA in Javascript (Node.js). I have tried to do the same thing in C++ and it works as expected:
...ANSWER
Answered 2020-Feb-21 at 16:15Your issue is caused by an integer overflow. A unint32_t is an integer of fixed size 2^32 bits. 0x9e3779b9 * 15 is 39816536535 which is approx 2^35.
This means you get an overflow as the memory location is simply not big enough to hold your number. Javascript does not have this problem as its not statically typed and the size allocated in memory will increase dynamically to hold it.
Use a larger datatype for C++, like an unsigned long or size_t (alias for unsigned long on most systems). Preferably use auto to let the compiler decide for you:
QUESTION
I'm following the guide Building The Library, but I have errors. My steps.
1. Set enviroment for x64 with vcvars64.bat.
ANSWER
Answered 2019-May-26 at 23:09It seems that the error was in the directory, which did not exist
C: \ Program Files (x86) \ Windows Kits \ 10 \ include \ 10.0.18362.0 \ ucrt;
I uninstalled the other Windows Kits to solve the problem. And it was already possible to compile Botan.
QUESTION
When I run this:
...ANSWER
Answered 2018-Jul-02 at 11:32You are trying to use mcrypt's algorithm name in openssl functions, which won't work, because mcrypt and openssl are different extensions. Also RIJNDAEL_256 does not have a direct counterpart in openssl. See another question for more details.
QUESTION
I'm using magento, when I load the page I get the following error:
...ANSWER
Answered 2018-Jun-05 at 11:24It's probably due to your magento version not being compatible with your php version.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install xTea
short reads (Illumina and Linked-Reads) 1.1 latest version git clone https://github.com/parklab/xTea.git 1.2 cloud binary version git clone --single-branch --branch release_xTea_cloud_1.0.0-beta https://github.com/parklab/xTea.git
long reads (PacBio or Nanopore) git clone --single-branch --branch xTea_long_release_v0.1.0 https://github.com/parklab/xTea.git
pre-processed repeat library used by xTea (this library is used for both short and long reads) wget https://github.com/parklab/xTea/raw/master/rep_lib_annotation.tar.gz
gene annotation files are downloaded from GENCODE. Decompressed gff3 files are required. For GRCh38 (or hg38), gff3 files are downloaded and decompressed from https://www.gencodegenes.org/human/release_33.html ; For GRCh37 (or hg19), gff3 files are downloaded and decompressed from https://www.gencodegenes.org/human/release_33lift37.html ; Or use the latest version
xtea is a bioconda package, to install first make sure the bioconda channel has been added:.
Use Conda xtea is a bioconda package, to install first make sure the bioconda channel has been added: conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge Then, install xtea (while creating a new enviroment): conda create -n your_env xtea=0.1.6 Or install directly via: conda install -y xtea=0.1.6
Install-free If the dependencies have already been installed, then install-free mode is recommended. One can directly run the downloaded python scripts.
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