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Recent Replies
Comment: C.reinhardtii single-cell Seurat object - gene names instead of loci
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GenoMax
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> BD Rhapsody protocols
That is important to know. Perhaps the issue is with the way you converted the GFF3 to GTF. What software did you …
Comment: C.reinhardtii single-cell Seurat object - gene names instead of loci
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Ana
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Thank you for your answer!
Unfortunalety, NCBI doesn't have the latest version of the genome and annotations for this organism (v6.1), so I…
Comment: Has anybody worked with C.reinhardtii single-cell before and could help me get t
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It is always safer to get sequence/annotations from standard sources like NCBI/Ensembl so no manipulations are required to make the data wo…
Comment: MultiQC_report
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Moved this to an answer since it seems to be a logical explanation for the observation reported in original post.
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Looking at the size distribution the data must already be pre-trimmed so it does not make sense to trim again. You should merge data from t…
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I think it just counts the total number of lines while there could be multiple adapters types per sample (ex : illumina_universal_adapter, …
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If your reference has invalid bases then you can get quite unexpected behaviors.
I am not sure what takes place - probably the scoring is…
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I got it figured out, thanks!
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Since only tools available (confirmed by @colindaven ) require illumina reads you would be basically creating "illumina like" reads from yo…
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I would use a tool like cyvcf2
https://brentp.github.io/cyvcf2/
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As in fragmenting (and pairing) the hifi reads? Do you think this would have any improvement over actual illumina reads?
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Thanks for confirming the absence of a tool, I think I can give up the hunt now. I've often done it this typical way of polishing after; ho…
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One problem that I encounter if I don't trim reads is that taxonomic classification of untrimmed reads often produces incorrect results. Th…
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Can you share the command you are using?
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