search

YangLab / CIRCexplorer

A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, Cell (2014), 159:134-147)
http://yanglab.github.io/CIRCexplorer
Other
60 stars 23 forks source link

Unique mapping with TopHat-Fusion #13

Closed smm19900210 closed 8 years ago

smm19900210 commented 8 years ago

unique mapping with TopHat-Fusion, tophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search hg19_bowtie1_index tophat/unmapped.fastq, can i use bowtie2 to mapping with TopHat-Fusion?

xingma commented 8 years ago

Yes, you can use bowtie2 as command below:

tophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --no-coverage-search hg19_bowtie2_index tophat/unmapped.fastq

However, it may be faster by bowtie1 than bowtie2 as the http://ccb.jhu.edu/software/tophat/fusion_index.shtml said.

smm19900210 commented 8 years ago

thank a lot! I will try it!

smm19900210 commented 8 years ago

hi xingma, i used your programes to identify circRNA, Start to convert fustion reads... Converted 5169 fusion reads! Start to annotate fusion junctions... Annotated 0 fusion junctions! Start to fix fusion junctions... Fixed 0 fusion junctions! there are zero circRNA, The ribo− RNA-seq is used.and RNase R treatment is performed. what's the matter with it?

kepbod commented 8 years ago

I don't recommend use TopHat-Fusion with bowtie2 as suggested in TopHat source codes.