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Hi,
I'm currently trying to use the CogentAP pipeline to process some bulk rna seq from murine sorted cells. We used the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (v3) for library prep, which generates UMI stranded libraries, and then sequenced on NextSeq (2x100bp 50million reads). Keen to get the CogentAP pipeline to work as it apparently demultiplexes and analyses in one go.
My issue is in generating an Illumina sample sheet! Am using the Illumina Exp Manager programme but it needs a bespoke Sample Prep Kit .txt file generated for the SMARTer kit I used - I feel this is highly liable to go wrong as it's not clear what information is required. Has anyone done this before?? Any advice or pitfalls?? I realise it's a bit of a long shot.
Thanks!!
I'm currently trying to use the CogentAP pipeline to process some bulk rna seq from murine sorted cells. We used the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (v3) for library prep, which generates UMI stranded libraries, and then sequenced on NextSeq (2x100bp 50million reads). Keen to get the CogentAP pipeline to work as it apparently demultiplexes and analyses in one go.
My issue is in generating an Illumina sample sheet! Am using the Illumina Exp Manager programme but it needs a bespoke Sample Prep Kit .txt file generated for the SMARTer kit I used - I feel this is highly liable to go wrong as it's not clear what information is required. Has anyone done this before?? Any advice or pitfalls?? I realise it's a bit of a long shot.
Thanks!!