CIRCexplorer2 for paired end data

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5.2 years ago

archana.bioinfo87 ▴ 210

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 • 906 views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 5.2 years ago by archana.bioinfo87 ▴ 210

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What have you tried?

ADD REPLY • link 5.2 years ago by Ram 43k

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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.

ADD REPLY • link updated 5.2 years ago by Ram 43k • written 5.2 years ago by archana.bioinfo87 ▴ 210

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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.

ADD REPLY • link 5.2 years ago by Ram 43k

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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

ADD REPLY • link 5.2 years ago by archana.bioinfo87 ▴ 210

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