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Recent Replies
Comment: Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
by
Kevin Blighe
72k
Cross-posted: https://support.bioconductor.org/p/9136520/
Answer: sequence similarity
by
Joe
19k
If your sequences are already aligned and/or the same length, or you do not want to align them, you can use some simple edit distance measu…
Comment: Loading PCA - different value depending on the package used
by
Bastien Hervé
4.9k
I did not see it at first, but the Loadings of the first PC are in `e-n` which make the loading values super small. These genes are not the…
Answer: Tassel5v2 vcf file with 'N' in reference and alternate allele
by
Lindsay
•
0
I believe eight loci in your above example are all deletions. In the VCF specification, to indicate an insertion or deletion you also have…
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
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