lemurRepair

Lemur Repair Study

Directories to include

• XR-seq_pipeline
• RNA-seq_pipeline
• TCR
• Orthology
• Circos
• XR-seq_simulation

Preprocessing RNA-seq and XR-seq reads

XR-seq

Required software

bowtie2-2.3.4.1
samtools-1.9
bedtools2-2.27.1
cutadapt-1.9.1

1. Define parameters in align_xr.sh

   • GENOME_DIR: reference fasta file
   • BOWTIE2_IND: bowtie2 index directory
   • SAMPLE: full path of fastq file (without .fastq exstension)

2. Run align_xr.sh

Output files will be located at where input files are

RNA-seq

Required software

star-2.6.1
bedtools2-2.27.1

1. Define parameters in make_star_index.sh

   • RefGenome: reference fasta file
   • Annotation: reference gtf file
   • STARGENOMEDIR: output path for star index

2. Run make_star_index.sh

3. Define parameters in align_rna.sh

   If your samples are SingleEnd simply leave blank Pair2

   • STARGENOMEDIR: star index from previous step
   • Pair1
   • Pair2
   • SAMPLE: output prefix

XR-seq_simulation

TODO:ART simulation. @vogulcan

Required software

go-1.14

1. Compile filter_syn.go

GOOS=linux go build main.go

2. Run filter_syn -h for all command line parameters

TCR

Required software

python-3.7.4
bedtools2-2.27.1
plotly-4.1.0

1. Run tcr.py for both human and mouse lemur

Simple usage:

python tcr.py --biomart mart_lemur.txt --out ./lemur

This will create two bed files for TSS and TES, if above script sample is used filenames will be lemur_tss.bed and lemur_tes.bed

2. Define parameters in tcr_bedtools.sh

   • SAMPLE: full path of aligned bed file (without _cutadapt_sorted.bed exstension, by default it's same as SAMPLE parameter in XR-seq alignment step)
   • TSS: TSS bed file from previous step (without .bed exstension)
   • TES: TES bed file from previous step (without .bed exstension)
   • GENOME: tab seperated file fith chromosome names and lengths

This step will produce two bed files ${SAMPLE}_tcr.bed and ${SAMPLE}_shuffled_tcr.bed

3. To plot results run plot_tcr.py after defining file paths for all human and lemur, tss and tes tcr bed files inside plot_tcr function