Question: Circexplorer2 Star outputs

24 months ago by

gayatri281 • 0 wrote:

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!!!

rna-seq • 790 views

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modified 24 months ago by Kevin Blighe ♦ 71k • written 24 months ago by gayatri281 • 0

24 months ago by

Kevin Blighe ♦ 71k

Republic of Ireland

Kevin Blighe ♦ 71k wrote:

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

ADD COMMENT • link written 24 months ago by Kevin Blighe ♦ 71k

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!!

ADD REPLY • link written 24 months ago by gayatri281 • 0

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

ADD REPLY • link written 24 months ago by Kevin Blighe ♦ 71k

Parsing

Annotating

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