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Recent Replies
Comment: Annotation Issue using miRBASE gff
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anthony.santana.703.j
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Hello Geno,
You dont understand how much I appreciate you, but yes I used featureCounts my trimming is correct my leniancy on those trim f…
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Your code looks ok (although I can't check the data manipulations that are specific to your own dataset). The analysis you have done is bas…
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> I looked online the according to everything the gff from miRBASE should have been compatible.
I looked at the GFF file from miRBase an…
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Hi, just wanted to ask if you've got any answers?
Comment: Annotation Issue using miRBASE gff
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As awlays Geno, thank you so much for helping, although I thought the same thing, I looked online the according to everything the gff from …
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You can't mix and match genome sequence and annotations. If you used a prebuilt bowtie index from NCBI then you will need to find an annota…
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Generally, fold-changes can be hard to distinguish from TPMs between samples when TPM variability between genes is large. Gene-wise scaling…
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Generally, they are equivalent. They both are designed to handle spliced reads (e.g. RNA-seq) well.
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[M::mm_idx_gen::73.687*1.32] collected minimizers
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Thanks for the prompt response!
* min: 67, max: 93,862, avg: 3,626, q25: 2737, q75: 4406
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Is there anything in `ragtag.scaffold.asm.paf.log` file?
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> the average read length in my ONT library is ~3Kbp
What is the range of read lengths in this dataset? Was this run on a minION or larger…
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Not sure I fully understand your question. Many of us use the local computer as a dumb terminal to get to the HPC where much of the work ha…
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Yes, from my laptop I do the final reports with graphs, etc and all the code is source controlled with git. I am not computing anything on …
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Show example images and the code used to generate them. We can't see what you see, so it's hard to say if you are plotting things incorrect…
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