5.Sort alignments by 可对Track区域进行排序,如想返回最初结果则选择 Re-pack alignments即可;
6.默认情况下Track Alignments 区以左图紧凑的单个 reads 的形式展示,通过 View as pairs 可成对显示,且中间以细线连接 (右图);
在左图中按住Ctrl 键鼠标左击某一个长条 (a read),将以相同的彩色颜色显示出与其配对 (paired mate) 的另一条 read。黑色的表示没有与之配对的另一条read。选中一条 read 后右键 Go to Mate将会跳转到与其配对 (paired mate) 的另一条 read。If the paired reads have a large insert size, the paired mate will not be highlighted. 右键选择Clear Selections 来清除所有选择的reads。同时注意到不同reads会用不同的颜色表示 (蓝色:插入大小小于期望值;红色:插入大小大于期望值;绿色、青色、深蓝色:倒置、重复、易位事件),更多详情见:Interpreting Color by Insert Size 和 Interpreting Color by Pair Orientation;低分辨率下在 Track Alignments 区域选择Color alignments by >> insert size and pair orientation 时比对的reads会显示不同的颜色 (Red have larger than expected inferred sizes, and therefore indicate possible deletions; Blue have smaller than expected inferred sizes, and therefore indicate insertions;实心灰代表比对质量比较高的测序片段,空心灰代表比对到此处的测序片段也可以比对到其他位点。),高分辨率下,可以精确到每个位点的碱基类型:当比对序列上与参考基因组相同的超过80%时,用灰色表示;否则用红色-T,蓝色-C,绿色-A,橙色-G;Translocations on the same chromosome can be detected by color-coding for pair orientation, whereas translocations between two chromosomes can be detected by coloring by insert size.
7.Paired-end alignment tracks 时 (View as pairs),右键选择 View mate region in split screen 可分隔显示;可实现多个分隔;在下图①处右键选择 Switch to standard view 或鼠标左键双击可返回单个分区;
5. 察看可变剪切情况
1.Loaded junctions data in the standard .bed format (例如TopHat’s “junctions.bed”等输出文件);
6.1 Mutation Files:MAF (mutation annotation format) and MUT (mutation)文件;
6.2 VCF Files
1.Each bar across the top of the plot shows the allele fraction for a single locus.
2.The genotypes for each locus in each sample. Dark blue = heterozygous, Cyan = homozygous variant, Grey = reference. Filtered entries are transparent.