Question: Circexplorer2 Star outputs
0
gravatar for gayatri281
24 months ago by
gayatri2810
gayatri2810 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
ADD COMMENTlink modified 24 months ago by Kevin Blighe71k • written 24 months ago by gayatri2810
0
gravatar for Kevin Blighe
24 months ago by
Kevin Blighe71k
Republic of Ireland
Kevin Blighe71k 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 COMMENTlink written 24 months ago by Kevin Blighe71k

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 REPLYlink written 24 months ago by gayatri2810

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 REPLYlink written 24 months ago by Kevin Blighe71k
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