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David Ray's lab scripts

Table of Contents:

Description

The purpose of this repository is to share the most common scripts and protocols used by the Ray's lab members.

As members of this group, we can edit and comment all the scripts submitted here as needed.

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Please Tag your scripts with their corresponding key word, so they can be grouped properly

Key words:

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  • TEs analysis
  • Genome analysis (includes assembly and annotation)
  • Transcriptome analysis (includes assembly and annotation)
  • Basic tools (example: manipulate and edit fasta files )
  • Selection analysis
  • Homology analysis

How to create a note?

Here it is a cool and easy to follow tutorial for HackMD, which uses Markdown Syntax Reference.

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This repository is public, so do not post any passwords or important information for your projects!

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Ray's lab
Scripts used for TEs, genome, transcriptome analysis, and more...
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Multiple Genomes Alignment

Author: Diana Moreno Santillan dmorenos@ttu.edu Date: August 2020 This pipeline performs multiple genome alignments and consists in three main steps: Perform pairwise alignments with lastz. Alignment sensitivity and specificity improvement with Michael Hiller's Genome Alignment Tools chain/net pipeline. Multiple genome alignment with multiz-TBA tool. Table of Contents [TOC]

Apr 22, 2021
TE curation analysis, post RAM

This is a plan for examining the output of RepeatAfterMe, a TE consensus extension pipeline. Create four new folders bad, good, long, odd, inverted_LTR Each putative TE will have five files associated with it. .out - a subset of the larger RepeatMasker.out file telling you what TEs, if any, are present. .png - a graphical representation of the alignment of 40+ hits and the consensus extended.fa - an alignment of 40+ hits and the consensus rep.fa - the consensus generated by RAM for this putative element

Apr 22, 2021
**Genome assembly: Flye software**

Author Diana Moreno (dmorenos@ttu.edu) Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. It takes raw PB / ONT reads as input and outputs polished contigs. Table of Contents [TOC] Flye usage: :::info

Apr 22, 2021
Bat1k de novo TE curation

RepeatModeler on each assembly, masked using final mammal library - March, 2021 - see /lustre/scratch/daray/bat1k_TE_analyses/rmasker/_RM_Ns mkdir /lustre/scratch/daray/bat1k_TE_analyses/rmodeler-newinstall_Ns cd /lustre/scratch/daray/bat1k_TE_analyses/rmodeler-newinstall_Ns Process RepeatModeler output to eliminate short (<100 bp) consensi. Cat with mammal TE library. mkdir cdhit_analysis find . -type f -name "*_N_consensi.fa" | xargs cp -t cdhit_analysis/

Apr 22, 2021
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