User: kc

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kc0
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Posts by kc

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Comment: C: strand specific RNA-seq mapping for bacterial transcriptomics
... Thank you all for your comments! It seems like there isn't a lot of open-source pipelines/workflows for bacterial RNAseq. I know of [Rockhopper][1] (standalone app but hard to extract mappings, etc to do other analyses) and [SPARTA][2] (which does not take strand-specific) Are there any other bacte ...
written 3 months ago by kc0
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Comment: A: strand specific RNA-seq mapping for bacterial transcriptomics
... For BWA I suppose we should use BWA-MEM but would there be any specific flags required for strand specific paired-end RNAseq reads? Thank you. ...
written 3 months ago by kc0
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strand specific RNA-seq mapping for bacterial transcriptomics
... Hi Was wondering which would be the best mapper for strand-specific RNA-seq mapping for bacterial transcriptomics? And are there specific flags to indicate? Thank you. ...
rna-seq written 3 months ago by kc0
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Comment: C: understanding contig statistics
... Hi Brian Would you advise a different quality filtering/trimming pipeline for going into taxonomic profiling instead of assembly? ...
written 8 months ago by kc0

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