parameters for stranded cDNA

[alexyfyf]

Hi team,

Thanks for developing this tool. I'm wondering what parameters would I use for stranded cDNA Nanopore data?
I saw the --rna flag which disables checking on both strands. Is it suitable to use in that case? And will this speed up the clustering?

Thanks a lot for helping with this.
Cheers,
Alex

[eileen-xue]

Hi Alex,

--rna is for RNA data. Not using this parameter will let RATTLE process cDNA data.

RNA mode is faster than cDNA mode since it only checks one strand and the clustering results are different.

Best,
Eileen

[EduEyras]

Let me add you can use --rna with the stranded cDNA data. Indeed, the analysis is the same, simply not checking both strands, only the forward strand from the input. best E.

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On Fri, 9 Dec 2022 at 09:26, Eileen Xue ***@***.***> wrote: Hi Alex, --rna is for RNA data. Not using this parameter will let RATTLE process cDNA data. RNA mode is faster than cDNA mode since it only checks one strand and the clustering results are different. Best, Eileen — Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKBYM6PYHNNU4NOETFY3WMJ4ERANCNFSM6AAAAAASYW52IU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[alexyfyf]

Thank you so much for providing this suggestion.

[tann5er]

Hi there.

I used pychopper to reorient the reads such that first-strand cDNA reads where reverse complimented so that all the reads in the dataset maintain the original mRNA transcript sequence (where U=T obviously). Should I use the --RNA flag for clustering?

[EduEyras]

Yes, that would be the right option for clustering Thanks E.

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On Sat, 20 May 2023 at 22:09, tann5er ***@***.***> wrote: Hi there. I used pychopper to reorient the reads such that first-strand cDNA reads where reverse complimented so that all the reads in the dataset maintain the original mRNA transcript sequence (where U=T obviously). Should I use the --RNA flag for clustering? — Reply to this email directly, view it on GitHub <#41 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCZKB4HDQMXIMFJUIYUV53XHCYA3ANCNFSM6AAAAAASYW52IU> . You are receiving this because you commented.Message ID: ***@***.***>