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Recent Replies
Comment: Understanding the ColData Matrix
by
Friederike
6.9k
Like so:
```
> sample_info <- data.frame(condition = c(rep("SNF2",5), rep("WT",5)), row.names = names(readcounts) )
> sample_info
co…
Comment: Transcript enrichment in Illumina RNAseq
by
Friederike
6.9k
Are you trying to understand the different library preparation methods that are typically used for bulk RNA-seq? This [review paper by Grif…
Comment: RRBS ANNOTATION
by
giovannaventola3es9
▴
30
thaks a lot.
However, Then the annotation what is the correct pipeline?
Thanks.
Comment: RRBS ANNOTATION
by
Papyrus
▴
740
Well that really would depend on the specifics of your project, the analyses that will be performed downstream, etc. and there is no one tr…
Answer: protein-protein interaction analysis
by
Michael Dondrup
48k
STRING is a curated database (DB) as you state correctly. Now, for the following we can totally abstract from the nature of items in the DB…
Answer: DEG list turn into keggscape
by
Kozo
▴
10
Hello, I am the developer of KEGGscape.
Can I ask you to show me an example of that DEG list?
If I have that example, I might be able t…
Comment: How to get output of annotated genes from ChIPseeker tool
by
EES
▴
20
Thank you! Is there any option in ChIPseeker to write overlapped genes?
Comment: Gigabase Clarification (Same as Gigobyte?)
by
joe_genome
▴
10
Perfect, thanks for the clarification on this in such a detailed mannar. I appreciate it quite a lot, definitely points me in the right dir…
Comment: Gatk bam metrics
by
Sabeen
•
0
i used the same reference file for bwa alignment and here for CollectAlignmentSummaryMetrics
Comment: sequence similarity
by
Sej Modha
4.9k
Another tool that can be used and is much faster is [MMSeqs2][1].
[1]: https://github.com/soedinglab/MMseqs2
Comment: Loading PCA - different value depending on the package used
by
camillab.
▴
40
Thank you, I wrote an email to the developer of `FactorMineR` long time ago and he said that "There is no way to use the PCA function with…
Comment: RRBS ANNOTATION
by
giovannaventola3es9
▴
30
ah ok I understand.
Thanks for your great explanation.
However, I have a list of CpG positions (.txt files) for several samples (3 replicat…
Answer: How to calculate bam coverage apart from Qualimap?
by
ATpoint
48k
The tool does not produce (the expected) output because you are not using the correct syntax/options.
`genomecov` expects the input via `…
Comment: Do I need to assume differences in coverage profile when I compare the first rea
by
GenoMax
100k
Unless a significantly different library preparation method was used the first read from a paired-end library should be equivalent to a lib…
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