User: Friederike

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Friederike1000
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3 years ago
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

http://abc.med.cornell.edu/

Posts by Friederike

<prev • 119 results • page 1 of 12 • next >
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Answer: A: Gene-level vs. Transcript-level quantification
... There's a difference between the read alignment step (which needs the actual sequence) and the quantification (which basically just counts the numbers of reads overlapping with defined loci, i.e., genes or transcripts). The standard workflow for model organisms with well established genome sequences ...
written 21 hours ago by Friederike1000
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Comment: C: How to filter RNAseq Data for being constant in all three biological replicates
... >how to rely on it being deferentially expressed That's what the (adjusted) p-values are for. ...
written 22 hours ago by Friederike1000
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Answer: A: Understanding Illumina Hisq Output
... While Pierre and h.mon have addressed all your questions, I just wanted to pick up your assumption that > the different sets of files are from different flow cells Without knowing the actual samples that you sequences, we cannot completely extract all the information you may need. There are va ...
written 1 day ago by Friederike1000
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Comment: C: How to filter RNAseq Data for being constant in all three biological replicates
... I would be surprised if DESEq et al would call the example that you showed above differentially expressed although it, of course, also depends on the values from the other condition. If those values were considerably higher (e.g., 1000, 1200, 900), I'd still think that your gene in question could b ...
written 1 day ago by Friederike1000
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Comment: C: How to filter RNAseq Data for being constant in all three biological replicates
... >to not include transcripts in the differential expression analysis that are different in replicates I implore you to *not* do this manually. This is exactly what the tools I linked above are trying to do *for* you -- and they've had a decade of development! ...
written 1 day ago by Friederike1000
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Answer: A: How to filter RNAseq Data for being constant in all three biological replicates
... To identify genes that are consistently different in the 3 replicates of your controls versus the 3 replicates in your experiment, use the packages that have been developed for differential gene expression analysis. [limma][1], [edgeR][2] and [DESeq2][3] have all been developed to exactly address th ...
written 1 day ago by Friederike1000
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Answer: A: Analyzing RNA-seq without replicates
... The approach you describe seems very reminiscent of the paired experimental design as described, for example, in the [edgeR user manual (section 3)][1]. I strongly recommend you try that approach (or use [DESeq2][2] with the appropriate design formula). [1]: https://www.bioconductor.org/packages ...
written 10 days ago by Friederike1000
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Comment: C: Normalization of single cell RNA-seq data with different read depths
... Were your biological samples each sequenced separately, i.e., is the library size effect confounded with the different conditions you wish to compare? I'm not a big fan of subsampling, precisely because of the data loss, but you will have to filter quite stringently nevertheless. E.g., you could on ...
written 15 days ago by Friederike1000
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Comment: C: Is the RNA-seq library indeed strand-specific?
... interesting...what organism is this? did you notice any other problems with this data set, e.g. after running FastQC? [QoRTs][1] also has a script that checks strand-specificity, would be interesting to see what it spits out for those data sets. [1]: https://hartleys.github.io/QoRTs/ ...
written 16 days ago by Friederike1000
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Comment: C: Count the fragments from BAM file
... >I'm interested in using BAM information in counting what do you actually mean? The answer to the question you've framed ("How do I count the fragments from BAM files") has been given with featureCounts. Are you, in fact, interested in _understanding_ the BAM file entries? ...
written 21 days ago by Friederike1000

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