ATACProc | ATAC-seq processing pipeline | Genomics library

 by   ay-lab Shell Version: 2.0 License: No License

kandi X-RAY | ATACProc Summary

kandi X-RAY | ATACProc Summary

ATACProc is a Shell library typically used in Artificial Intelligence, Genomics applications. ATACProc has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Supervisors: Dr. Ferhat Ay and Dr. Pandurangan Vijayanand. La Jolla Institute for Immunology, CA 92037, USA.
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              ATACProc has a low active ecosystem.
              It has 12 star(s) with 8 fork(s). There are 2 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 2 open issues and 0 have been closed. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of ATACProc is 2.0

            kandi-Quality Quality

              ATACProc has no bugs reported.

            kandi-Security Security

              ATACProc has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              ATACProc does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              ATACProc releases are available to install and integrate.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
            Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of ATACProc
            Get all kandi verified functions for this library.

            ATACProc Key Features

            No Key Features are available at this moment for ATACProc.

            ATACProc Examples and Code Snippets

            No Code Snippets are available at this moment for ATACProc.

            Community Discussions

            QUESTION

            search for regex match between two files using python
            Asked 2022-Apr-09 at 00:49

            I´m working with two text files that look like this: File 1

            ...

            ANSWER

            Answered 2022-Apr-09 at 00:49

            Perhaps you are after this?

            Source https://stackoverflow.com/questions/71789818

            QUESTION

            Is there a way to permute inside using to variables in bash?
            Asked 2021-Dec-09 at 23:50

            I'm using the software plink2 (https://www.cog-genomics.org/plink/2.0/) and I'm trying to iterate over 3 variables.

            This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file.

            The idea is to iterate over the input files and then over exclude files to generate single outputfiles.

            1. Input files: Highland.ped - Midland.ped - Lowland.ped
            2. Exclude-map files: HighlandMidland.txt - HighlandLowland.txt - MidlandLowland.txt
            3. Output files: HighlandMidland - HighlandLowland - MidlandHighland - MidlandLowland - LowlandHighland - LowlandMidland

            The general code is:

            ...

            ANSWER

            Answered 2021-Dec-09 at 23:50

            Honestly, I think your current code is quite clear; but if you really want to write this as a loop, here's one possibility:

            Source https://stackoverflow.com/questions/70298074

            QUESTION

            BigQuery Regex to extract string between two substrings
            Asked 2021-Dec-09 at 01:11

            From this example string:

            ...

            ANSWER

            Answered 2021-Dec-09 at 01:11

            use regexp_extract(col, r"&q;Stockcode&q;:([^/$]*?),&q;.*")

            if applied to sample data in your question - output is

            Source https://stackoverflow.com/questions/70283253

            QUESTION

            how to stop letter repeating itself python
            Asked 2021-Nov-25 at 18:33

            I am making a code which takes in jumble word and returns a unjumbled word , the data.json contains a list and here take a word one-by-one and check if it contains all the characters of the word and later checking if the length is same , but the problem is when i enter a word as helol then the l is checked twice and giving me some other outputs including the main one(hello). i know why does it happen but i cant get a fix to it

            ...

            ANSWER

            Answered 2021-Nov-25 at 18:33

            As I understand it you are trying to identify all possible matches for the jumbled string in your list. You could sort the letters in the jumbled word and match the resulting list against sorted lists of the words in your data file.

            Source https://stackoverflow.com/questions/70112201

            QUESTION

            Split multiallelic to biallelic in vcf by plink 1.9 and its variant name
            Asked 2021-Nov-17 at 13:56

            I am trying to use plink1.9 to split multiallelic into biallelic. The input is that

            ...

            ANSWER

            Answered 2021-Nov-17 at 09:45

            QUESTION

            Delete specific letter in a FASTA sequence
            Asked 2021-Oct-12 at 21:00

            I have a FASTA file that has about 300000 sequences but some of the sequences are like these

            ...

            ANSWER

            Answered 2021-Oct-12 at 20:28

            You can match your non-X containing FASTA entries with the regex >.+\n[^X]+\n. This checks for a substring starting with > having a first line of anything (the FASTA header), which is followed by characters not containing an X until you reach a line break.

            For example:

            Source https://stackoverflow.com/questions/69545912

            QUESTION

            How to get the words within the first single quote in r using regex?
            Asked 2021-Oct-04 at 22:27

            For example, I have two strings:

            ...

            ANSWER

            Answered 2021-Oct-04 at 22:27

            For your example your pattern would be:

            Source https://stackoverflow.com/questions/69442717

            QUESTION

            Does Apache Spark 3 support GPU usage for Spark RDDs?
            Asked 2021-Sep-23 at 05:53

            I am currently trying to run genomic analyses pipelines using Hail(library for genomics analyses written in python and Scala). Recently, Apache Spark 3 was released and it supported GPU usage.

            I tried spark-rapids library start an on-premise slurm cluster with gpu nodes. I was able to initialise the cluster. However, when I tried running hail tasks, the executors keep getting killed.

            On querying in Hail forum, I got the response that

            That’s a GPU code generator for Spark-SQL, and Hail doesn’t use any Spark-SQL interfaces, only the RDD interfaces.

            So, does Spark3 not support GPU usage for RDD interfaces?

            ...

            ANSWER

            Answered 2021-Sep-23 at 05:53

            As of now, spark-rapids doesn't support GPU usage for RDD interfaces.

            Source: Link

            Apache Spark 3.0+ lets users provide a plugin that can replace the backend for SQL and DataFrame operations. This requires no API changes from the user. The plugin will replace SQL operations it supports with GPU accelerated versions. If an operation is not supported it will fall back to using the Spark CPU version. Note that the plugin cannot accelerate operations that manipulate RDDs directly.

            Here, an answer from spark-rapids team

            Source: Link

            We do not support running the RDD API on GPUs at this time. We only support the SQL/Dataframe API, and even then only a subset of the operators. This is because we are translating individual Catalyst operators into GPU enabled equivalent operators. I would love to be able to support the RDD API, but that would require us to be able to take arbitrary java, scala, and python code and run it on the GPU. We are investigating ways to try to accomplish some of this, but right now it is very difficult to do. That is especially true for libraries like Hail, which use python as an API, but the data analysis is done in C/C++.

            Source https://stackoverflow.com/questions/69273205

            QUESTION

            Aggregating and summing columns across 1500 files by matching IDs in R (or bash)
            Asked 2021-Sep-07 at 13:09

            I have 1500 files with the same format (the .scount file format from PLINK2 https://www.cog-genomics.org/plink/2.0/formats#scount), an example is below:

            ...

            ANSWER

            Answered 2021-Sep-07 at 11:10

            QUESTION

            Usage of compression IO functions in apache arrow
            Asked 2021-Jun-02 at 18:58

            I have been implementing a suite of RecordBatchReaders for a genomics toolset. The standard unit of work is a RecordBatch. I ended up implementing a lot of my own compression and IO tools instead of using the existing utilities in the arrow cpp platform because I was confused about them. Are there any clear examples of using the existing compression and file IO utilities to simply get a file stream that inflates standard zlib data? Also, an object diagram for the cpp platform would be helpful in ramping up.

            ...

            ANSWER

            Answered 2021-Jun-02 at 18:58

            Here is an example program that inflates a compressed zlib file and reads it as CSV.

            Source https://stackoverflow.com/questions/67799265

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install ATACProc

            Following packages / libraries should be installed before running this pipeline:.
            Python 2.7
            R environment (we have used 3.4.3) User should also install the following R packages, by running the following command inside R prompt: install.packages(c(“optparse”, “ggplot2”, “data.table”, “plotly”)) Also user needs to install the bioconductor package GenomicRanges https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html
            Bowtie2 (we have used version 2.3.3.1) http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
            samtools (we have used version 1.6) http://samtools.sourceforge.net/
            PICARD tools (we have used 2.8.14 version now; previously we were using version 2.7.1) https://broadinstitute.github.io/picard/
            Utilities "bedGraphToBigWig", "bedSort", "bigBedToBed", "hubCheck" and "fetchChromSizes" - to be downloaded from UCSC repository http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/
            deepTools (we have used version 2.0) https://deeptools.readthedocs.io/en/develop/
            MACS2 (we have used version 2.1.1) https://github.com/taoliu/MACS
            HOMER (we recommend using the latest version) http://homer.ucsd.edu/homer/
            The package ataqv (https://github.com/ParkerLab/ataqv). User needs to download the GitHub release (.tar.gz) file in a convenient location, extract it, and provide corresponding path in a configuration file (mentioned below).
            Regulatory genomics toolbox (https://www.regulatory-genomics.org/) First user needs to install the module RGT using the following commands: pip install --user cython numpy scipy pip install --user RGT A folder rgtdata would be created inside the home directory. Next step is to configure that folder by typing the following commands: cd ~/rgtdata python setupGenomicData.py --hg19 python setupGenomicData.py --hg38 python setupGenomicData.py --mm9 python setupGenomicData.py --mm10 (Note: it is better to run the last four commands together in a qsub / cluster environment, otherwise it'll be time consuming). Then, user needs to set up the motif configuration data, via executing the following commands (preferable to run in qsub / cluster environment) cd ~/rgtdata python setupLogoData.py --all
            sambamba (we have used version 0.6.7) http://lomereiter.github.io/sambamba/
            IDRCode (https://drive.google.com/file/d/0B_ssVVyXv8ZSX3luT0xhV3ZQNWc/view?usp=sharing). User should unzip the archieve and store in convenient location. Path of this archieve is to be provided for executing IDR code.

            Support

            For any queries, please generate a GitHub issue, or alternatively, e-mail us:.
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries
            CLONE
          • HTTPS

            https://github.com/ay-lab/ATACProc.git

          • CLI

            gh repo clone ay-lab/ATACProc

          • sshUrl

            git@github.com:ay-lab/ATACProc.git

          • Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link