sRNA pipeline for paired data

[dorothyzh]

Hi Coud I use the code like this?

pRNASeqTools srna --adaptor "AAAAAAAAAAAAAA" --control control=Col_0_1_1.fq.gz,Col_0_1_2.fq.gz+Col_0_2_1.fq.gz,Col_0_2_1.fq.gz

The adaptor has already been removed, but the pRNASeq does not allow empty parameters after the adaptor, so I use AAAAAA
It seems like the "srna" cannot accept paired data.
###Mapping control_1...
Please provide the correst seq file! at /home/xialab/software/pRNASeqTools/Function.pm line 92.

Thanks

[grubbybio]

You may just omit the “—adaptor” parameter, then the adaptor removal will be skipped. Yes, “srna” only needs the first mate.

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2025年2月7日 12:30，Huan ZHONG ***@***.***> 写道： Hi Coud I use the code like this? pRNASeqTools srna --adaptor "AAAAAAAAAAAAAA" --control control=Col_0_1_1.fq.gz,Col_0_1_2.fq.gz+Col_0_2_1.fq.gz,Col_0_2_1.fq.gz The adaptor has already been removed, but the pRNASeq does not allow empty parameters after the adaptor, so I use AAAAAA It seems like the "srna" cannot accept paired data. Thanks — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFCDDLXDBBT3X2F5CSLM5WD2OQZIDAVCNFSM6AAAAABWVC2T2OVHI2DSMVQWIX3LMV43ASLTON2WKOZSHAZTOMRRGE4TKNQ>. You are receiving this because you are subscribed to this thread.

[dorothyzh]

I tried to omit ---adaptor, but the error occurs

Use of uninitialized value $adaptor in string eq at /home/xialab/software/pRNASeqTools/mode/srna.pm line 96.
Please specify the 3' adaptor! at /home/xialab/software/pRNASeqTools/mode/srna.pm line 96

[grubbybio]

Did you update the pipeline to the latest version?

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2025年2月9日 11:51，Huan ZHONG ***@***.***> 写道： I tried to omit ---adaptor, but the error occurs Use of uninitialized value $adaptor in string eq at /home/xialab/software/pRNASeqTools/mode/srna.pm line 96. — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFCDDLRNSVXWWH2FDRSCJV32O3GFPAVCNFSM6AAAAABWVC2T2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNBWGA2TIMJRGI>. You are receiving this because you commented.