User: Assa Yeroslaviz

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Assa Yeroslaviz1.2k
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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 • 366 results • page 1 of 37 • next >
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Comment: C: keep chromosome names in a bigwig file
... thanks for the suggestion. IMHO this is also not really a fixed solution, but just a different way to dodge the problem. Previously it was possible to access them using the command `names(bigWigList[[1]])` because they were saved with the data. ...
written 10 days ago by Assa Yeroslaviz1.2k
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Comment: C: keep chromosome names in a bigwig file
... I have figured out I can get them by calling them as such > levels(bigWigList[[1]]@metadata$ranges@seqnames) [1] "chrI" "chrII" "chrIII" "chrIV" "chrIX" "chrV" "chrVI" [8] "chrVII" "chrVIII" "chrX" "chrXI" "chrXII" "chrXIII" "chrXIV" [15] "chrXV" "ch ...
written 10 days ago by Assa Yeroslaviz1.2k
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keep chromosome names in a bigwig file
... after an update of the rtracklyer package, I loose the names of chromosomes in my bigwigfile object. I have a list of bigwig files, I'm reading into R for processing. filesList <- list.files(path = "./bigWigFiles",pattern = ".bw", full.names = TRUE) bigWigList <- lapply(X = filesList ...
rtracklayer bigwig import.bw written 10 days ago by Assa Yeroslaviz1.2k
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Comment: A: Analyzing ChIP-seq without input
... Thanks a lot for both answers(@ATpoint, @jared.andrews07). What would be than the advantage of having a data set with no controls? Why does MACS need the option to analyze data without the input samples? Can these samples cause a bias of my results? I am aware of the problem with stating a number ...
written 16 days ago by Assa Yeroslaviz1.2k
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Analyzing ChIP-seq without input
... I was wondering if anyone can tell me what is the advantages and disadvantages of doing a ChIP-Seq experiment with input samples (as oppose to no control samples). We have had a discussion today whether or not it make sense to use input samples in the normalisation process and what it would mean to ...
chip-seq normalisation written 16 days ago by Assa Yeroslaviz1.2k
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Comment: C: understanding bowtie2 unmapped reads
... I ran the files wiith fastq_screen against multiple indexed genomes. It didn't find any disconcerting results. In my experience ~50% is not a good mapping results. I can live with it, but I would like to know why it didn't map. I don't think it is the AB. Sample IP_IgG1 was also the one with the l ...
written 6 weeks ago by Assa Yeroslaviz1.2k
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understanding bowtie2 unmapped reads
... I have a ChIP-Seq data set with 4 IP and and Input samples as well as two IgG samples. When mapping the fastq samples (pair-end samples), I get very good results for the Input samples, but very bad results for the IgG samples and slightly better ones fro the IP samples: Input1 | 93.61% Inpu ...
bowtie2 fastq unmapped-reads written 6 weeks ago by Assa Yeroslaviz1.2k • updated 6 weeks ago by lieven.sterck5.5k
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Comment: C: velvetg failed during the assembly
... great answer. This has saved my run too. thanks a lot ...
written 7 weeks ago by Assa Yeroslaviz1.2k
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Comment: C: Waddington optimal transport for single-cell analysis
... sorry for the late reply. do you have experiene with the wot algorithm? I have reduced the quantile to 0.01 and still got empty files. Only when reducing the number of genes (creating a random subset) i manage to get some cell. Can you explain to me, based on what parameters/factors the cells are g ...
written 12 weeks ago by Assa Yeroslaviz1.2k
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Comment: C: comparing an assembly against close relatives
... thanks, I'll try it and see where it goes. ...
written 3 months ago by Assa Yeroslaviz1.2k

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Popular Question 10 days ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
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Scholar 3 months ago, created an answer that has been accepted. For A: Approximate matching to find similar DNA sequence
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Popular Question 5 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Student 7 months ago, asked a question with at least 3 up-votes. For estimation of size factors in DESeq2 analysis
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Popular Question 16 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Student 16 months ago, asked a question with at least 3 up-votes. For estimation of size factors in DESeq2 analysis
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