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use firehose_get to download TCGA data
Download data from TCGA
Comment: Importing a fastq file
EdgeR - relationship between logFC and coefficients
Answer: EdgeR - relationship between logFC and coefficients
Detecting highly variable genes within replicates
Detecting highly variable genes within replicates
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Comment: LncRNA Nomenclature
by
jain72744
▴ 10
My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs? lncRNA_transcripts <- getBM(attributes …
Answer: DESeq2 error
by
ATpoint
82k
At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
Comment: When should I use R-MarkDown over R-Script ?
by
ATpoint
82k
Why particular question? Rmarkdown is a composite of markdown and code. You can nicely separate free text, explanation, comments etc. from…
Comment: LncRNA Nomenclature
by
ATpoint
82k
RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
Comment: EdgeR - relationship between logFC and coefficients
by
gBioStar5
▴ 10
Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients
by
Gordon Smyth
★ 7.1k
Results presented by topTags() are on the log2 scale. Coefficients stored internally in the DGELRT object are on the loge scale. If you con…
Answer: Importing a fastq file
by
size_t
▴ 120
run command `explorer.exe .` in wsl terminal, and then drag file to folder
Comment: Contig assembly task, errors
by
Philipp Bayer
8.4k
Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
Comment: absolute path for symbolic links in Snakefile
by
Jesse
▴ 770
That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
Comment: Truncated metadata file report from ENA Portal API
by
GenoMax
142k
Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length
by
marco.barr
▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length
by
Pierre Lindenbaum
161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length
by
marco.barr
▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
Comment: Different output for read length
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marco.barr
▴ 100
I just published my link on paste, why can't I see my public paste on the site?
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