User: kristoffer.vittingseerup

Reputation:
420
Status:
Trusted
Location:
European Union
Last seen:
2 days, 15 hours ago
Joined:
2 years, 11 months ago
Email:
k***********************@bio.ku.dk

Posts by kristoffer.vittingseerup

<prev • 77 results • page 1 of 8 • next >
1
vote
0
answers
137
views
0
answers
Comment: C: Are 2 replicates per sample sufficient for RNA-seq data analysis?
... I dont think so - sounds quite strange. Did you look at the p-value distribution? Lastly to answer the question usually at least 3 replicates are recommended. ...
written 2 days ago by kristoffer.vittingseerup420
1
vote
0
answers
89
views
0
answers
Available non-TCGA matched tumor non tumor RNASeq/microarray data
... I'm on the lookout for publicly available matched tumor non tumor RNA-seq or microarray data - which is not from TCGA (biopsy based, not cell-lines). Do you know of any such dataset? Bonus points if it is available through recount2. ...
microarray rna-seq written 6 days ago by kristoffer.vittingseerup420
0
votes
1
answer
113
views
1
answers
Comment: C: available subcutaneous adipose RNA-seq
... You can download the quantifications for the individual samples [here][1]. [1]: https://gtexportal.org/home/datasets ...
written 27 days ago by kristoffer.vittingseerup420
0
votes
1
answer
113
views
1
answers
Answer: A: available subcutaneous adipose RNA-seq
... The GTEx consortium have you covered - according to [this][1] there are 442 samples in relase 7 [1]: https://gtexportal.org/home/eqtls/tissue?tissueName=Adipose_Subcutaneous ...
written 5 weeks ago by kristoffer.vittingseerup420
0
votes
1
answer
152
views
1
answers
Comment: C: Gene set enrichment analyses of different samples of the same species
... To do an enrichment test on your data you need to define two things: 1) What conditions do you want to compare? 2) What subset of genes do you want to test for enrichment of differen gene-sets (and compared to what)? Could you elaborate on both of these I can easily help you out :-) ...
written 5 weeks ago by kristoffer.vittingseerup420
2
votes
2
answers
325
views
2
answers
Answer: A: Exon coordinates and sequence
... If your data is form GENCODE the easiest is simply to download the corresponding FASTA file from gencodeGenes - [here][1] is the link to the most recent human release but it is important you select the right release. Alternatively I've used [Cufflinks gffRead][2] to extract the sequences of a GTF f ...
written 5 weeks ago by kristoffer.vittingseerup420
2
votes
2
answers
151
views
2
answers
Answer: A: RNA-Seq data avaliability online
... Most journals these days have it as a requirement that the raw (and more and more also processed) data is made publically available - it always say so in the article. Most data ends op on [geo][1] but I have also seen some RNAseq end up on [ArrayExpress][2] (counterintuitive to the name). There ar ...
written 5 weeks ago by kristoffer.vittingseerup420
0
votes
1
answer
140
views
1
answers
Comment: C: Differential gene expression anaylsis -Ballgown
... Only if you want to annotate the transcript to actually know which genes they belong to ...
written 5 weeks ago by kristoffer.vittingseerup420
1
vote
3
answers
190
views
3
answers
Answer: A: Quantifying mRNA level
... If you work with human data I would recomend the [GTEx protal][1] where you can se the gene expression across most tissues [1]: https://gtexportal.org/home/ ...
written 5 weeks ago by kristoffer.vittingseerup420
0
votes
0
answers
122
views
0
answers
Comment: C: Poly(A) tail 5'/3' biais
... You need to be a bit more specific - I'm not sure what you are asking...? ...
written 5 weeks ago by kristoffer.vittingseerup420

Latest awards to kristoffer.vittingseerup

Scholar 4 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 5 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 7 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 775 users visited in the last hour