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Recent Replies
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
rfran010
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1.5k
Generally, fold-changes can be hard to distinguish from TPMs between samples when TPM variability between genes is large. Gene-wise scaling…
Comment: HISAT2 or STAR
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rfran010
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Generally, they are equivalent. They both are designed to handle spliced reads (e.g. RNA-seq) well.
HISAT2 may be better if you are on a m…
Comment: Error Scaffolding with RagTag
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[M::mm_idx_gen::73.687*1.32] collected minimizers
[M::mm_idx_gen::75.834*1.84] sorted minimizers
[M::main::75.834*1.84] loaded/built the in…
Comment: Identify transgene insert loci/copy number in nanopore De-novo assembly
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Thanks for the prompt response!
* min: 67, max: 93,862, avg: 3,626, q25: 2737, q75: 4406
* minION
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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…
Comment: How to deal with intermediate files
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ramiro.barrantes
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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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> One simpler way that is closer is for example to mount the locations on our HPC to my laptop and hence not having to transfer anything
A…
Comment: How to deal with intermediate files
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Thank you!! I am aware of all of those, however, they are not exactly what I am looking for: I could transfer data from one place to anothe…
Comment: Best pairwise alignment for insertion and deletion-containing sequences
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rbpdee
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Thanks, @patrickdm! Let me give it a shot.
Answer: Best pairwise alignment for insertion and deletion-containing sequences
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patrickdm
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Hello, I'd try tweaking the [Affine Gap Scores][1] of Align.PairwiseAligner(), and if those are not good enough, consider the possibilty to…
Comment: How to deal with intermediate files
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Fair point about the sensitivity of data. I don't work on human or other particularly sensitive data so never really thought about it.
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Great list. Globus may be the perfect option, if it is already installed on HPC.
Something to consider before using any of the above. Not…
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