Hi there,
I have been seeing papers using CIRCexplorer2 with an unmapped.bam (paired-end) from TopHat2 that has then been converted to a single FASTQ file (using bedtools), before input into TopHat-Fusion, and subsequently CIRCexplorer2 parse(without --pe flag). Is this recommended? If not, should tophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search hg19_bowtie1_index read_1.fastq read_2.fastq be used with CIRCexplorer2 parse --pe?
Hi there, I have been seeing papers using CIRCexplorer2 with an unmapped.bam (paired-end) from TopHat2 that has then been converted to a single FASTQ file (using bedtools), before input into TopHat-Fusion, and subsequently
CIRCexplorer2 parse(without --pe flag). Is this recommended? If not, shouldtophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search hg19_bowtie1_index read_1.fastq read_2.fastqbe used withCIRCexplorer2 parse --pe?Thanks for the help.