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Recent Replies
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
•
0
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…
Comment: Is anticancer action of HDAC inhibitors - cancer cells specific or it may cause
by
GenoMax
100k
While you may get an answer, this question is out of scope for this (mainly) bioinformatics focused forum. You should ask this on biology s…
Comment: RRBS ANNOTATION
by
Papyrus
▴
740
Yes, this relates to a "problem" which does not have a unique solution, and is usually solved depending on the specific project. When we de…
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