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Andres S. Espindola andrese52

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andrese52 / EprobeCuration.md
Last active April 11, 2018 03:05
Eprobe curation

E-probe design and curation

Blast of e-probes with nt

blastn -task blastn -query eprobes.fasta -db nt -out e-probes.txt -num_threads 12
BlastCheck.pl -c raw-eprobes.fasta -i blast_output.txt -p output_name -f common,names,comma,separated,without,spaces
@andrese52
andrese52 / RNA_seq_analysis.md
Last active March 22, 2018 03:52
Wheat RNA sequencing microbiome analysis

RNAseq data analysis pipeline

Notes: 1.) When running jobs, always keep an eye on the scheduler. Some jobs may warrant requests for walltime extensions. 2.) Always check your output files for error messages to ensure your job completely correctly. 3.) Always double check your scripts. Files WILL overwrite.

download raw data and back up immediately

  1. Trimomatic -run separately for each replicate pair
#!/bin/bash
@andrese52
andrese52 / Blast.md
Last active June 8, 2018 17:11
Blast.md

Creating a blast database

makeblastdb -in genome.fasta -parse_seqids -dbtype nucl
blastn -task blastn -query eprobes.fasta -db genome.fasta -out coords.txt -num_threads 12 -outfmt 6
@andrese52
andrese52 / Anaconda.md
Last active May 16, 2018 15:03
Update Anaconda through the Anaconda prompt

Updating Anaconda

conda update conda
@andrese52
andrese52 / multiple-deploy-keys-multiple-private-repos-github-ssh-config.md
Last active September 16, 2019 23:24 — forked from gubatron/multiple-deploy-keys-multiple-private-repos-github-ssh-config.md
How to configure multiple deploy keys for different private github repositories on the same computer without using ssh-agent

Let's say alice is a github.com user, with 2 or more private repositories repoN. For this example we'll work with just two repositories named repo1 and repo2

https://github.com/alice/repo1

https://github.com/alice/repo2

You need to be to pull from these repositories without entering a passwords probably on a server, or on multiple servers. You want to perform git pull origin master for example, and you want this to happen without asking for a password.