User: kristoffer.vittingseerup

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2 years, 5 months ago
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Posts by kristoffer.vittingseerup

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Differences in FPKM values for same sample in multiple comparisons
... It happens because Cufflinks/Cuffdiff uses a statistical model where it considers all the data you supply. Since you provide differen input data the results are different. Use the contrast function as suggested by @Satya below. ...
written 2 days ago by kristoffer.vittingseerup190
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Comment: C: RNAseq Analysis using RUVs
... I'm not sure what your question is. Are you asking about RUV normalization before DE analysis of the groups or are you asking about normalization for another DE analysis? In the later case could you elaborate on what that is? ...
written 3 days ago by kristoffer.vittingseerup190
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Comment: C: GeneAnalytics or IPA?
... Just remember also add a propper background (all the genes you tested for differential expression) else your results are not valid. ...
written 6 days ago by kristoffer.vittingseerup190
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Comment: C: Amino acids conservation score
... Could you elaborate on what you mean by aligned. To orthologous or to the genome or...? ...
written 9 days ago by kristoffer.vittingseerup190
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Answer: A: RNA-seq analysis between 2 closely related strains of the same species
... I'm assuming you dont have a reference genome due to the non-model organisme comment (if you have you should take a different approach). The other possible approach you could do would be to do a de-novo assembly based on the pooled data and then quantify that in each of your samples. Both approac ...
written 6 weeks ago by kristoffer.vittingseerup190
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Comment: C: Why does RNA sequencing data has Thymine as opposed to Uracil? Theoretically, it
... I think Its much more useull to have it as T since that allows direct mapping to the genome ...
written 6 weeks ago by kristoffer.vittingseerup190
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Answer: A: download CNV file for breast cancer BRCA from TCGA website
... You can find a CNV file for each cancer patient [here][1] (around 1100). For each patient there are 4 files: Two of them are with and without masked regions according to [this][2]. The two files for for each region appear to be different versions of the analysis (F10 vs F11) which I cannot find wh ...
written 6 weeks ago by kristoffer.vittingseerup190
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Comment: C: Bowtie2 map results ? and very low number of Peaks in ChIP seq data?
... Could you correct all copy/paste mistakes - its very hard to help without that :-). Fx "5096777 pairs aligend concordantly **XX** times". ...
written 7 weeks ago by kristoffer.vittingseerup190
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Answer: A: DEXseq alternative splicing detection
... I think they take the 5'/3' difference and test that as a separate exon. In other words they split an exon into two smaller sub-exons and testing each of them separately. Do however note that this only works for quite large changes as you need reads (30-100nt) that maps uniquely to the regions you t ...
written 7 weeks ago by kristoffer.vittingseerup190
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Answer: A: Combining RNA-Seq and ChIP-Seq
... **1**: That is a good hypothesis - but you cannot be sure that is the way it happens (the difference between [correlation and causation][1]). To really show that you would need to go into the lab and do some experiments that affected the POU1F1's ability to bind to your gene and then observe the gen ...
written 7 weeks ago by kristoffer.vittingseerup190

Latest awards to kristoffer.vittingseerup

Scholar 5 weeks ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species

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