snandiDS
commented
1 year ago Hi, Sorry for the late reply, Yes, that's an issue. We are planning to get a new version addressing these issues. Will let you know once it is done.
On Sat, Sep 17, 2022 at 9:18 AM mariusmihasan @.***> wrote:
I am attempting to use the prokseq-v2.0 pipeline to evaluate some data obtained by directly sequencing RNA using an nanopore device ( ONT MinION). I can test-run the pipeline using the provided data, samples.bowtie.PEsample and param.bowtie.yaml files. However, the pipeline fails to process my MinION data. I believe that the culprit is the much lower quality ( mean Phred of 7) that the MinION data has, hence AfterQC treats all my rna seq data as bad. Is there a way to bypass the AfterQC step and feed the data directly in the next step - mapping with bowtie2? Are there any other details that I should be aware of when processing my ONT MinION rna-seq data? Thanks
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I am attempting to use the prokseq-v2.0 pipeline to evaluate some data obtained by directly sequencing RNA using an nanopore device ( ONT MinION). I can test-run the pipeline using the provided data, samples.bowtie.PEsample and param.bowtie.yaml files. However, the pipeline fails to process my MinION data. I believe that the culprit is the much lower quality ( mean Phred of 7) that the MinION data has, hence AfterQC treats all my rna seq data as bad. Is there a way to bypass the AfterQC step and feed the data directly in the next step - mapping with bowtie2? Are there any other details that I should be aware of when processing my ONT MinION rna-seq data? Thanks