Osama Shiraz Shah osamashiraz
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| # USEFUL CODE FOR R PLOT THEMES | |
| `%notin%`=Negate(`%in%`) | |
| library(magrittr) | |
| library(ggplot2) | |
| library(cowplot) | |
| library(dplyr) | |
| library(EnvStats) | |
| library(ggpubr) |
osamashiraz
/ rna_seq_variant_pipeline.sh
Created
April 12, 2019 16:43
— forked from PoisonAlien/rna_seq_variant_pipeline.sh
RNA seq Variant calling pipeline according to gatk best practices
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| #!/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 |
osamashiraz
/ gatk_bundle_and_WGS_test_data.sh
Created
April 1, 2019 15:33
— forked from ShujiaHuang/gatk_bundle_and_WGS_test_data.sh
Common datasets for GATK
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| #Known datasets: GATK bundle for human b37 reference | |
| # | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz.md5 |
osamashiraz
/ gist:a18647716b9d3d62fad8a39f37fe39f8
Created
February 28, 2019 05:55
Running Jupyter bash kernel on Windows 10 (Using WSL)
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| 1. Install Anaconda on Windows 10 | |
| 2. Get jupyter notebook and install bash kernel from here: https://github.com/takluyver/bash_kernel, make sure to run "python -m bash_kernel.install" | |
| 3. Install WSL and install pip3. | |
| 5. Using pip3 install python3, ipython3 and bash_kernel in WSL (follow same link as above for the bash kernel installation, make sure to run "python -m bash_kernel.install") | |
| 6. Make sure when you run "python3 -m bash_kernel" on WSL it shows a message saying: | |
| NOTE: When using the `ipython kernel` entry point, Ctrl-C will not work. | |
| To exit, you will have to explicitly quit this process, by either sending | |
| "quit" from a client, or using Ctrl-\ in UNIX-like environments. |