As I am trying to use CIRCexplorer2 but little bit confuse that what command is perfect for my paired-end data.
If anyone has some hint please let me know.
Any help is much appreciated.
What have you tried?
CIRCexplorer2 align -G /mnt/c/Users/ark446/share/hg19_kg.gtf -i /home/archana87/bow_tie_build_hg19/hg19 -j /home/archana87/bowtie2_index/hg19 -f Sample.fastq > CIRCexplorer2_align.log
I am wondering for paired-end data. Maybe it is a silly question but I am confused.
The manual says you need to pick a different aligner for PE reads. Please read this other page in the manual that has options to skip alignment steps when you align with a different tool.
Thanks for the reply. I got the answer that
a. You could offer multiple fastq files (or compressed files) separated or comma.
b. Only single-read RNA-seq is supported. It is recommended to convert paired-end RNA-seq to single-read RNA-seq before alignment