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CIRCexplorer2 for paired end data

Hi,

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.

Thanks

rna-seq
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updated by Ram Ram • written by archana.bioinfo87 archana.bioinfo87

What have you tried?

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written by Ram Ram 
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.

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updated by Ram Ram • written by archana.bioinfo87 archana.bioinfo87

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

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written by archana.bioinfo87 archana.bioinfo87

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