Table 1. Bioinformatic codes used.
| Program | Function | Code used |
|---|---|---|
| V3C-seq analysis | ||
| Bowtie2 | Alignment | bowtie2 --trim5 50 --very-sensitive -x/storage/htc/ biocompute/ircf/dbase/genomes/M_musculus/bowtie2/ index/mm10 -S 24hpi_1.sam 24hpi_1.fastq |
| Samtools | Sam to Bam | samtools view -b -S -o aligned_24hpi_1.bam 24hpi_1.sam |
| Sort | samtools sort -o aligned_sorted_24hpi_1.bam aligned_24hpi_1.bam | |
| BEDtools | Compute histogram | genomeCoverageBed -ibam aligned_sorted_24hpi_1.bam -bg - trackline -split -g. ..>24hpi_1.bedgraph |
| ChIP-seq analysis | ||
| Bowtie2 | Alignment | bowtie2 -x/storage/htc/biocompute/ircf/dbase/genomes/M_musculus/ bowtie2/index/mm10 -U 16hpi_gh2ax_1.fastq -S 16hpi_gh2ax_1.sam |
| Samtools | Sam to Bam | samtools view -b -S -o aligned_16hpi_gh2ax_1.bam 16hpi_gh2ax_1.sam |
| Sort | samtools sort -o aligned_sorted_16hpi_gh2ax_1. bam aligned_16hpi_gh2ax_1.bam |
|
| BEDtools | Bam to BED conversion | bedtools bamtobed -i 16hpi_gh2ax_1.bam>16hpi_gh2ax_1.bed |
| EPIC | Peak Calling | epic -t 16hpi_gh2ax_1.bed -c 16hpi_ip.bed -gn mm10 -b BED -o epic_12hpi_gh2ax_1 |
| BEDtools | Intersection | bedtools intersect –a 16hpi_gh2ax_1.bed –b 16hpi_gh2ax_2. bed>16hpi_gh2ax_1_2.bed |
| Jaccard analysis | bedtools jaccard -a mock_gh2ax.bed -b 16hpi_gh2ax.bed | |