User: benjyrolls

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benjyrolls70
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Posts by benjyrolls

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Comment: C: Variants Calling on RNA Seq Samples
... ok, does this mean on the mutations from the p53 knockout are significant in this case since the Wild Type mice could be identical ? Will it be worth considering the mutaions from the two KO replicates in terms of the effect of p53 KO ? i have attached a sample output from the .vcf from one of the K ...
written 26 days ago by benjyrolls70
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Comment: C: Variants Calling on RNA Seq Samples
... i am trying to figure the effect of the p53 knockout on the deferentially expressed genes and whether the deferentially expressed genes are linked to a specific biological process. However, in my RNA Seq pipeline there is an option to check for variants, i wanted to understand the meaning of those v ...
written 26 days ago by benjyrolls70
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Variants Calling on RNA Seq Samples
... hello I have 4 RNA Seq samples from p53 wild type mouse(WT) and p53 knock out(KO) mouse (2 replicates each) which were treated with Tamoxifen . these were analysed with sam tools to call variants. Variants were called for each of the WT and KO samples.(4 .vcf files) my question is even though v ...
variant calling samtools rna-seq written 26 days ago by benjyrolls70
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Comment: C: Finding Primary Motif from Genomic DNA data
... Hi Kennethcondon2007 thanks for your question , after performing MACS2 on my ChIP-Seq data. I used galaxy to extract the genomic DNA then imported these to Centrimo http://meme-suite.org/tools/centrimo for further analysis. ...
written 4 weeks ago by benjyrolls70
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Finding Primary Motif from Genomic DNA data
... Hello I have a genomic DNA data in fasta format which I have exported to MEME CHIP suite to find the motifs in this data. This has presented me with the p-values and E-values for the known Motifs and have come up with https://ibb.co/conksa, I would like to plot or come out with a plot of Bits and Z ...
chip-seq written 4 weeks ago by benjyrolls70 • updated 4 weeks ago by kennethcondon2007790
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Interpreting Differentially Expressed Genes(DEGs) from RNA Seq experiment
... I have a list of Differentially Expressed Genes(DEGs) from an experiment which involved a mouse model with Sox2 and another model with Sox2 Knock Out( Sox2 WT vs Sox2 KO). What conclusions can I make from these DEGs and what can I say of these genes in terms of Sox2 ? thanks Benjy ...
rna-seq written 5 weeks ago by benjyrolls70 • updated 4 weeks ago by igor4.3k
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Answer: A: Cancer expression data sets
... Have a look at this , might help http://biogps.org/dataset/tag/cancer/ ...
written 8 weeks ago by benjyrolls70
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Interpreting Chip Seq Results
... Hello I performed a ChIP Seq experiment and performed these steps MACS, CEAS, Gene Ontology Enrichment with GREAT . I have some enriched terms as well as enriched pathways such as PTEN Signalling pathway, WNT pathway etc. From my information how can I find the genes which are up or down regulated ...
macs2 chip-seq ceas great written 8 weeks ago by benjyrolls70 • updated 8 weeks ago by Devon Ryan68k
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Comment: C: Upstream Regulator Gene Differential expression
... As per you statement "Checking for known binding sites in the majority of the DE genes should reasonably suffice for this." I have performed a check on the binding sites and this is what I [found][1] Sox2 seems to be regulating some genes in conjunction with others? [1]: http://159.149.160.88 ...
written 9 weeks ago by benjyrolls70
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Comment: C: Upstream Regulator Gene Differential expression
... There are 3 replicates. Well, I was trying to reproduce the results in [this experiment][1] using the RNA-Seq data however am not confident in the differentially expressed genes and its role to Sox2 in terms of RNA-Seq. However in the ChIp-Seq experiment, Centrimo motif analysis, using the Chip-Se ...
written 9 weeks ago by benjyrolls70

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Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Cancer expression data sets

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