GitHub - KatalinaBobowik/Epi_Study: Metatranscriptome analysis of pathogens within whole blood of an Indonesian cohort

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Metatranscriptome analysis of pathogens within whole blood of an Indonesian cohort

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Name		Name	Last commit message	Last commit date
Latest commit History 26 Commits
CleanScripts		CleanScripts
OldKnitr		OldKnitr
SnakemakePipelines		SnakemakePipelines
scripts		scripts
.gitignore		.gitignore
MethanocaldococcusJannaschii_STARMapping.sh		MethanocaldococcusJannaschii_STARMapping.sh
QC_Pipeline_ControlSamples.sh		QC_Pipeline_ControlSamples.sh
README		README

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# Folder created on 17.01.19 by Katalina Bobowik.

This folder contains scripts for analysing what pathogens are present in the Indonesian RNA seq data. All raw RNA seq reads can be found on Spartan within the folder: /data/cephfs/punim0586/shared/raw_data.


Files:

1) unmappedReads_DiamondMetagenomicClassification.sh: extracting unmapped reads from STAR bam files and running the metagenomic classifier Diamond. To run Diamond, all scripts were run via an array script (/data/cephfs/punim0586/kbobowik/Diamond/diamond_array_script.txt) using sbatch. The sbatch shell script can be found here: /data/cephfs/punim0586/kbobowik/EpidemiologicalSurvey/scripts/shell_scripts/Diamond_metagenomicAlignment.sh.

Programs used:
diamond version 0.9.10
samtools 1.9