tophat2-fusion 文档搬运工：https://ccb.jhu.edu/software/tophat/fusion_tutorial.shtml
###step1.tophat
1 | tophat2 -p 8 -o $OUTPUT --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search --fusion-anchor-length 10 --fusion-min-dist 100000 --mate-inner-dist 40 --mate-std-dev 100 $hg_bowtie1_index $read1.fastq.gz $read2.fastq.gz |
Note:
–fusion-search，融合 reads 搜索
–keep-fasta-order,
–bowtie1，使用 bowtie1 代替 bowtie2 进行 reads 比对。需要使用 bowtie-1.1.2，最新版本 1.2.2 会报错
–no-coverage-search,
–fusion-anchor-length 10 ,
–fusion-min-dist 100000 ,
–mate-inner-dist 40 ,
–mate-std-dev 100 ,
###step2.tophat-fusion-post
1 | tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 $hg_bowtie1_index |
Note:
–num-fusion-reads* , 支持融合的最少 reads 数目
–num-fusion-pairs, 支持融合事件的最少配对 reads 数，表示为跨越融合点的测序片段
–num-fusion-both, 支持融合的最少 reads，包括跨越的 reads 对和 split reads
–fusion-read-mismatches, Reads support fusions if they map across fusion with at most this many mismatches. The default is 2.
–fusion-multireads, Reads that map to more than this many places will be ignored. The default is 2.
–non-human, If your annotation is different from that of human, use the option.
–fusion-pair-dist, Pairs with this specified distance are counted as supporting evidence for the fusion. The default threshold for the inner distance is 250.
results
测试了多个样品，多个参数，也根据官网数据、命令运行项目，都没有发现任何融合结果，bug还是打开方式不对