Moderator: i.sudbery
i.sudbery ♦ 4.0k
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Posts by i.sudbery
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... Depending on which normalisation you've used (VST or rlog), I was under the impression that there should be no zeros, and thus no need for +1. In fact rlog should is already adding be a pseudocount and taking the log.
1,000,000 is chosen because it it the value that puts the numbers and a "human sc ...
written 2 hours ago by
i.sudbery ♦ 4.0k
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... I would either fit a negative binomial, using gene length as an offset (not a co-variate, you need to force the coefficient to 1). Unfortunately getting the gene length is not entirely trival as you need to know which transcripts are expressed. If you can run the original data through salmon, that w ...
written 3 days ago by
i.sudbery ♦ 4.0k
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Answer:
A: UMI Tools Dedup
... If you are doing drop-seq or 10x chromium, I highly recommend [`alevin`][1]. Other tools that can handle UMI deduplication are STARsolo, `umis` and `picard MarkDuplicatesWithCigar`. Not that the last two do not do error correction.
Two things might cause excessive memory usage:
1. Many reads whos ...
written 3 days ago by
i.sudbery ♦ 4.0k
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... If I understand your question correctly you are trying to test whether genes that are more highly conserved tend to be more highly (or lowly) expressed. Thus would want to do what is conceptually similar to a linear correlation with conservation on one access and expression in another?
Comparing ...
written 4 days ago by
i.sudbery ♦ 4.0k
0
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1
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106
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Comment:
C: Htseq-count result assistance
... And where did you get the genome reference (fasta) from. The one you used to align the reads? ...
written 5 days ago by
i.sudbery ♦ 4.0k
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Comment:
C: col as names
... I'm not sure what you mean by "the colnames of "my.names" are "3, 2, 3, 3, 3, 3...", with a row with the actual names I want"
but read.table will not accept colnames that start with a number. Only column with names that are valid R variable names are allowed. As you have seen though, you can force ...
written 6 days ago by
i.sudbery ♦ 4.0k
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... can you show us an outline of what this might look like for a single file? ...
written 6 days ago by
i.sudbery ♦ 4.0k
1
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1
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106
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1
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Comment:
C: Htseq-count result assistance
... Its possible nothing is wrong. You really need the full numbers. Depending on your GTF, most genes will have a count of zero, even in a good sample.... but how many can still be a mesaure of how good the sample is. If you are using the full ensembl GTF, which, I believe has about 50,000 genes in it, ...
written 6 days ago by
i.sudbery ♦ 4.0k
0
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1
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106
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Comment:
C: Htseq-count result assistance
... Hi @citynsukka I edit your post to make the list of counts format correctly. You can do this by highlighting the part of the post to be formatted as-is and pressing the code button (labelled 101010). I've also changed the category - the tool category is used to announce/promote new tools. ...
written 6 days ago by
i.sudbery ♦ 4.0k
1
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80
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... I think `pip --user` puts the binaries under `~/.local/bin` rather than `$HOME/bin`, so try the following in your `.bashrc`
export PATH=$HOME/.local/bin:$PATH
...
written 6 days ago by
i.sudbery ♦ 4.0k
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For A: Filtering during RNA Seq analysis?
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For A: How to only change/substitute every QNAME(Read ID) from a Bam file?
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For C: if I am right about miRNA DE workflow
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For A: Alternative to Cufflinks ?
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