Question: How do I specify single end Read in CIRCquant?
0
gravatar for jaqx008
4 weeks ago by
jaqx00860
jaqx00860 wrote:

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
ADD COMMENTlink written 4 weeks ago by jaqx00860

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

ADD REPLYlink modified 29 days ago • written 29 days ago by cschu1811.9k

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

ADD REPLYlink modified 29 days ago • written 29 days ago by jaqx00860

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

ADD REPLYlink written 29 days ago by cschu1811.9k

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

ADD REPLYlink written 28 days ago by jaqx00860

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!).

ADD REPLYlink written 28 days ago by cschu1811.9k

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

ADD REPLYlink written 28 days ago by jaqx00860
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