2 Mapping

Mapper: bowtie2

2.1 Table of mapping statistic

• NB, only uniqely mapped reads (i.e. excluding multi-mapped reads) were used in further analysis
• NB, one sample (M3V-INP) removed from the analysis

2.2 Boxplots of mapping staststic

2.2.1 No. of sequencing reads

Figure 2.1: No. of reads

2.2.2 No. of uniquely mapped reads

Figure 2.2: No. of unique mapped reads

2.2.3 Unique mapping rate

Figure 2.3: Unique mapping rate

2.2.4 Multi mapping rate

Figure 2.4: Multi mapping rate

2.2.5 Total mapping rate

Figure 2.5: Total mapping rate

2.3 BigWig files

• Note, each individual BAM files were merged (i.e. samtools merge file1 file2 …) by groups (FV, FD, MV, and MD).
• Therefore, there are 4 bigwig files.
• You can download from here.
• To visualize, download igv then import files above.