Circexplorer2 Star outputs

Question

[gayatri281]

Hi All, I am trying to run Circexplorer2 version 2.3.5 with Star output Chimeric.out.junction files. I have multiple samples.

The parsing step produces multiple bed files and annotation step produces outputs that have different number of circRNAs and ciRNAs. How should I combine these into a count table for differential expression analysis. Ideally shouldn't there be a single bed file. Am I missing something.

Here are my codes:

Parsing

for i in *Chimeric.out.junction; do time CIRCexplorer2 parse -t STAR $i -b $i.new.back_spliced_junction.bed > $i.CIRCexplorer2_parse.log ;done

Annotating

for i in *.back_spliced_junction.bed ; do CIRCexplorer2 annotate -r hg38_ref_all.txt -g hg38.fa -b $i -o  $i.Circexplorer2.txt ; done

 cat Sample_145_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk '{print $14}' | sort | uniq -c

19258 circRNA

612 ciRNA

 cat Sample_146_Chimeric.out.junction.new.back_spliced_junction.bed.Circexplorer2.txt | gawk '{print $14}' | sort | uniq -c

17791 circRNA

729 ciRNA

Thank you!!!

Answer 1

[Kevin Blighe]

I do not believe you are missing anything. CircExplorer2 has successfully run on your samples. It is now your decision about what to do with the results.

• Do you combine the output and look for common regions across all samples, or just groups of samples that are related?
• Do you just produce a 'master' table of all identified RNAs?

These questions only you can answer, an answer that will depend on what your hypotheses and aims are.

Kevin

[gayatri281]

Thank you for the help Kevin!!

I want to do the option 2. I want to produce a 'master' table of all identified RNAs for all samples.

However as the number of circRNAs are different for each sample, I am not sure what is the best way combine these tables together.

Thank you!!

[Kevin Blighe]

Hey, that is just an analysis decision that you will have to make. You could include only the common circRNAs,or all identified circRNAs