Enquiry on --stranded and --standpref argument usage in find_circ!

[cheehowteo]

Dear Marvin Jens,

Good day!

I am currently using the find_circ program developed by you for my work. I noticed there are additional arguments (--stranded & --strandpref). May I know the function of these two arguments?

I have single end RNA-seq reads and I would like to identify circRNAs using find_circ. Should I include the --stranded and --strandpref argument in my analysis?

Are these two argument only use for stranded specific paired end reads?

Thank you.

Best regards, Teo

[mschilli87]

@cheehowteo: AIAK, strandedness is related the the library preparation protocol, regardless if the resultung library is sequenced single- or parired-end. So you'll need to make sure with whoever prepared the libraries for your sequencing data. Nowadays, libraries typically are stranded though. If you cannot figure out the library preparation protocl you can also map the data to the genome and check the loci of a + and a - strand gene, each, using IGV: On a stranded procol, the coverage should be strongly biased towards one strand (and the opposite one for the two genes you check). On an unstranded one, one would expect the coverage to be about 50/50 on both strands for both genes.

[cheehowteo]

Dear Marvin Jens,

The sequence library of my RNA-seq is actually stranded specific 150 bp paired end reads. I converted the paired end read to single end read before feed the reads to find_circ. Do I need to include both --stranded --strandpref for my find_circ analysis? I was confused whether I should use these two arguments when I already mapped the reads to reference genome using stranded option in bowtie.

Thank you.

Best regards, Teo