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Recent Votes
A: Change sample names in vcf
Answer: very short 'time series' bulk rna-seq, testing two conditions
Comment: Is anticancer action of HDAC inhibitors - cancer cells specific or it may cause
Comment: Loading PCA - different value depending on the package used
Answer: Understanding the ColData Matrix
Answer: DEG list turn into keggscape
Answer: protein-protein interaction analysis
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Recent Replies
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: protein-protein interaction analysis
by
Heetak
• 0
So funny! XD
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 `…
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