User: Assa Yeroslaviz

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Assa Yeroslaviz1.3k
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AssaYeroslaviz
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I'm a bioinformatician in the bioinformatics group of the Max-Planck Institute for biochemistry in Munich, Germany. In our group we have a broad research focus that is mainly dedicated to help solving biological problems. We achieve this by a very close interaction with researchers in biological research labs, located here at the MPI-B in Munich, as well as in many other research institutions around the globe. Due to these close ties with a biological research environment, we are partly dedicating our efforts to the development of bioinformatics tools and databases that will help advance biological sciences.

Posts by Assa Yeroslaviz

<prev • 403 results • page 1 of 41 • next >
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Comment: C: bcl2fastq results in Poly-N in R1
... this might be the correct solution. thanks ...
written 4 hours ago by Assa Yeroslaviz1.3k
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Comment: C: bcl2fastq results in Poly-N in R1
... yes, but the QC is good ...
written 4 hours ago by Assa Yeroslaviz1.3k
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bcl2fastq results in Poly-N in R1
... Hi, we're working on a scRNA-Seq samples, where R1 has 16bases with the cellular and molecular barcodes, while R2 is 150bases long and contains the genomic sequence. This data set appears to be very problematic, as it shows many problems. We think that we have sequence into the adapter, as running ...
scrna-seq single-cell paired-end bcl2fastq rna-seq written 4 hours ago by Assa Yeroslaviz1.3k • updated 4 hours ago by genomax78k
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Comment: C: No rule keywords allowed after run in snakefile
... thanks for the advices. I have found it easier to handle the number of `threads` used, when I inout it once in the config file and not each time in every rule. Why is it better to set separately? The input and output have the same wildcard- `{IDS}`. The rest of the path point to where the data shou ...
written 6 days ago by Assa Yeroslaviz1.3k
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No rule keywords allowed after run in snakefile
... In my workflow I would like to have the option to choose which mapper to use. in my config file I have this statement mapper: "bowtie2" In the Snakefile I then have a mapping rule as such: mapper = config['mapper'] ... rule Mapping: input: R1='{IDS}.conc.R1.fas ...
run python snakemake written 6 days ago by Assa Yeroslaviz1.3k • updated 6 days ago by Thibault D.690
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Comment: C: GSEA PreRanked lists from DESeq2 results table
... This is exactly what I mean. Some people use this values, other use a different one, sometimes without any reason. Especially if the results are similar. The advantage of using the FC values is, that I don't have any `0` in the table. What do you do with them, if you convert to Signed log (nomin ...
written 10 days ago by Assa Yeroslaviz1.3k
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Comment: C: GSEA PreRanked lists from DESeq2 results table
... thanks for the link. it is a very god example. ...
written 10 days ago by Assa Yeroslaviz1.3k
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GSEA PreRanked lists from DESeq2 results table
... I have several tables of results from different DESeq2 runs. The next step would be to do GO enrichment or GSEA enrichment analysis. For that I would like to create a ranked list of genes for GSEAPreRanked. But I'm not sure which value to take for the ranking. Do I use the log2FC values or the p-v ...
fgsea deseq2 gsea preranked written 13 days ago by Assa Yeroslaviz1.3k • updated 11 days ago by jomo018540
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Comment: C: missing coeeficients in resultsNames(dds)
... This is not true. when I run this: > resMA <- lfcShrink(ddsMat, coef="design_D0_KO_low_vs_D0_KO_high", type="apeglm") using 'apeglm' for LFC shrinkage. If used in published research, please cite: Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for ...
written 4 weeks ago by Assa Yeroslaviz1.3k
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missing coeeficients in resultsNames(dds)
... I have the following design matrix > colData(ddsMat) DataFrame with 8 rows and 9 columns sample names day condition differentiated rep ReadSums design sizeFactor D0_MAEAKO_High_1 1 D0_MAEAKO_High_1 D0 KO high 1 71041314 D0_KO_high 0.80109874 D0_MAEAKO_High_2 2 D ...
deseq2 design written 4 weeks ago by Assa Yeroslaviz1.3k

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