Upendra Kumar Devisetty upendrak

## rna_seq_variant_pipeline.sh
#!/bin/bash
#
# AUTHOR: Anand M.
# RNA-Seq variant calling pieline accoring to GATK Best practices.
# https://www.broadinstitute.org/gatk/guide/article?id=3891
#
# Call with following arguments
# bash rna_seq_variant_pipeline.sh <Input_Reads1.fq.gz> <Input_Reads2.fq.gz> <output_basename>
#
# Assumes STAR aligner is under path

## understanding-word-vectors.ipynb

      
              1 file
            
          
              349 forks
            
          
              51 comments
            
          
              1435 stars
            
          
                aparrish
                / understanding-word-vectors.ipynb
            
            
              Last active
              April 29, 2024 17:57
            
              
                Understanding word vectors: A tutorial for "Reading and Writing Electronic Text," a class I teach at ITP. (Python 2.7) Code examples released under CC0 https://creativecommons.org/choose/zero/, other text released under CC BY 4.0 https://creativecommons.org/licenses/by/4.0/
              
          
      Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
          Viewer requires iframe.
      
    
## deseq2-analysis-template.R
## RNA-seq analysis with DESeq2
## Stephen Turner, @genetics_blog

# RNA-seq data from GSE52202
# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

# Import & pre-process ----------------------------------------------------

# Import data from featureCounts

## install-samtools-bcftools-and-htslib.md

      
              1 file
            
          
              7 forks
            
          
              8 comments
            
          
              20 stars
            
          
                adefelicibus
                / install-samtools-bcftools-and-htslib.md
            
            
              Last active
              April 3, 2024 20:49
            
              
                Install samtools, bcftools and htslib on linux
              
          
    Install Samtools, BCFTools and htslib on linux

Install some build dependencies

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libncurses5-dev
[samtools]


## rotate-axis-labels-ggplot2.R
# Adapted from https://stackoverflow.com/a/7267364/1036500 by Andrie de Vries

# This is it: theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

library(ggplot2)

td <- expand.grid(
  hjust=c(0, 0.5, 1),
  vjust=c(0, 0.5, 1),
  angle=c(0, 45, 90),

## maker_genome_annotation.md

      
              1 file
            
          
              45 forks
            
          
              33 comments
            
          
              93 stars
            
          
                darencard
                / maker_genome_annotation.md
            
            
              Last active
              March 7, 2024 08:50
            
              
                In-depth description of running MAKER for genome annotation.
              
          
    Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.
Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.
Software & Data

Software prerequisites:


RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (ver


## bamfilter_oneliners.md

      
              1 file
            
          
              51 forks
            
          
              17 comments
            
          
              153 stars
            
          
                davfre
                / bamfilter_oneliners.md
            
            
              Last active
              February 24, 2024 01:23
            
              
                SAM and BAM filtering oneliners
              
          
    SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)

@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)

  
## nextflow_tower.md

      
              1 file
            
          
              2 forks
            
          
              1 comment
            
          
              1 star
            
          
                tomsing1
                / nextflow_tower.md
            
            
              Created
              February 15, 2021 20:15
            
              
                Setting up nextflow tower locally
              
          
    Installing Nextflow on a Mac


Install JAVA 8

 brew install adoptopenjdk8


Install Nextflow: curl https://get.nextflow.io | bash in the current directory
Optional: Move the nextflow binary to a directory that is in the PATH.


## Snakefile
RUNS, = glob_wildcards("fastq/{run}_1.fastq.gz")

SALMON = "/proj/milovelab/bin/salmon-1.4.0_linux_x86_64/bin/salmon"

ANNO = "/proj/milovelab/anno"

rule all:
    input: expand("quants/{run}/quant.sf", run=RUNS)

rule salmon_index:

## dna_encode.py
# Copyright 2019 Hannes Bretschneider
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation
# files (the "Software"), to deal in the Software without
# restriction, including without limitation the rights to use,
# copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following
# conditions:
	#!/bin/bash
	#
	# AUTHOR: Anand M.
	# RNA-Seq variant calling pieline accoring to GATK Best practices.
	# https://www.broadinstitute.org/gatk/guide/article?id=3891
	#
	# Call with following arguments
	# bash rna_seq_variant_pipeline.sh <Input_Reads1.fq.gz> <Input_Reads2.fq.gz> <output_basename>
	#
	# Assumes STAR aligner is under path
	## RNA-seq analysis with DESeq2
	## Stephen Turner, @genetics_blog

	# RNA-seq data from GSE52202
	# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
	# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

	# Import & pre-process ----------------------------------------------------

	# Import data from featureCounts
	# Adapted from https://stackoverflow.com/a/7267364/1036500 by Andrie de Vries

	# This is it: theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

	library(ggplot2)

	td <- expand.grid(
	hjust=c(0, 0.5, 1),
	vjust=c(0, 0.5, 1),
	angle=c(0, 45, 90),
	RUNS, = glob_wildcards("fastq/{run}_1.fastq.gz")

	SALMON = "/proj/milovelab/bin/salmon-1.4.0_linux_x86_64/bin/salmon"

	ANNO = "/proj/milovelab/anno"

	rule all:
	input: expand("quants/{run}/quant.sf", run=RUNS)

	rule salmon_index:
	# Copyright 2019 Hannes Bretschneider
	#
	# Permission is hereby granted, free of charge, to any person
	# obtaining a copy of this software and associated documentation
	# files (the "Software"), to deal in the Software without
	# restriction, including without limitation the rights to use,
	# copy, modify, merge, publish, distribute, sublicense, and/or sell
	# copies of the Software, and to permit persons to whom the
	# Software is furnished to do so, subject to the following
	# conditions: