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Popular Question to
bioinfo
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Popular Question to
bk11
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1.8k
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Agamemnon
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satva72
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Recent Replies
Comment: Multi-factor designs in DiffBind
by
Ram
41k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: Where is the index command?
by
jkbonfield
★
1.2k
That's a tarball of the C source code you've just unpacked.
There's an "INSTALL" file with detailed instructions of how to compile the sof…
Comment: Multi-factor designs in DiffBind
by
g.persic1991
•
0
Hi Rory,
Thanks a lot for your comment.
Up to now I have performed the contrast in an explicitly way (as you suggest) using this comma…
Answer: How to avoid missannotated GO terms?
by
Istvan Albert
99k
The problem most likely is with the blast alignment.
BLAST is a local aligner, getting a hit to another sequence does not mean that the…
Comment: Read count vs Depth
by
Ram
41k
Do not use spreadsheet software to view plain text files. Use a plain text utility such as BBEdit/TextWrangler/NotePad++/gedit or simple co…
Comment: vcftools
by
Ram
41k
What output files were you expecting? Was nothing printed on the screen at all?
Comment: Consensus peaksets in DiffBind - conceptual questinos
by
Rory Stark
★
2.0k
The question of defaults for the software is often a tricky one.
I do think the mutliple-replicate method is a good idea in many cases, w…
Answer: How to query 1000 genomes project VCF files for specific regions without downloa
by
Pierre Lindenbaum
158k
bcftools works with remote indexed VCF
bcftools view "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_cov…
Comment: Consensus peaksets in DiffBind - conceptual questinos
by
Sam
▴
300
My question was not how to do it - but conceptually, should not this be the default way to do an analysis, unless there is a good reason *n…
Comment: select unique samples in R
by
bk11
★
1.8k
Instead of `setdiff(list1$Sample_ID, list2$Sample_ID)` do this-
`setdiff(list1, list2)`
Answer: Consensus peaksets in DiffBind - conceptual questinos
by
Rory Stark
★
2.0k
What you describe - deriving a consensus set comprising the union of peaks called in at least two replicates of any sample group - is exact…
Comment: select unique samples in R
by
Matthias Zepper
4.2k
Then you use the resulting IDs to subset your original data frame(s).
Comment: convert dataframe R
by
fracarb8
★
1.3k
You need to pass a column, so `id.vars = "rows"` should work.
Comment: convert dataframe R
by
satva72
•
0
Thanks. there is this error:
"Error in melt.data.table(data, id.vars = rownames(data)) :
One or more values in 'id.vars' is invalid."
T…
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