How do I specify single end Read in CIRCquant?

Question

[jaqx008]

Hey everyone, I am trying to identify circular RNAs in my seq data using CIRCquant. I have read and understood the usage and all the files required I have generated. However, my reads are single end reads and the usage and manual for CIRIquant do not provide any option for single end reads input even though in the published paper they mentioned that the program can take in signle end reads. can any one help ? thanks and see usage below for paired end reads

CIRIquant -t 20 --config ./chr1.yml -1 ./fastq1 -2 ./fastq2 --config ./chr1.yml --no-gene -o ./GCF -p GCFloc

[cschu181]

If this is the published paper (https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-019-0614-1), where do they mention that the program can take in single end reads?

Given that the method is based on (reverse) overlap detection of paired-end reads

RO read detection and verification is designed to detect RO reads from paired-end reads based on their 5′ reverse overlaps

feeding it single-end reads does not really make sense to me...

Edit: citation

[jaqx008]

this is the publication and they mentioned it here

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316645/#Sec18title under Optimal choice of parameters in CIRI

[cschu181]

Hmm, have you tried to only use the -1 option?

[jaqx008]

Yes it doesnt work. at this point I just assume its not possible. Thanks for trying to help.

[cschu181]

Just judging from the first couple lines of code at the CIRIquant github repo, the tool will terminate if it doesn't receive -1 and -2, so yea, not without modifying that (which might be easy enough, though!).

[jaqx008]

Yes I agree. I tested with a paired end it ran just fine.

Answer 1

[kevinzjy]

Hi jaqx, you can still use CIRI2 for identification of circRNAs from single end data, CIRIquant is designed for quantification of circRNAs based on alignment result of paired-end reads, and does not support single end reads yet.

By the way, our manuscript is still under review, I think what you mentioned is another tool CIRI-full, which is designed to detect internal splicing patterns of circRNAs.

[pbigbig]

Hi, I am sorry for some quick questions about CIRI2:

1. As I understand, CIRI2 can only be used for RNA-seq data that did not undergo polyA enrichment, isn't it?

2. Can I use CIRI2 to construct circRNAs from Small RNA-seq data?

Thank you!