User: Assa Yeroslaviz

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Assa Yeroslaviz1.2k
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Munich
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AssaYeroslaviz
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7 years, 8 months ago
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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 • 338 results • page 1 of 34 • next >
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Comment: C: fastqc of chipseq dataset - two peaks in GC content
... This I have also considered, but why don't I see it also in the overrepresented sequences section? Is it possible that the adapter are so GC (or more G)-rich, that it skew the results so much? ...
written 2 days ago by Assa Yeroslaviz1.2k
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Comment: C: fastqc of chipseq dataset - two peaks in GC content
... I haven't trimmed it yet. the sequencing was done a a nextseq with dual indexing. About the trimming - do I just trim the first bases of the read (hard trim) or should I look for the barcodes (soft trim)? ...
written 2 days ago by Assa Yeroslaviz1.2k
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fastqc of chipseq dataset - two peaks in GC content
... We are running a ChIP-Seq experiment of multiple samples on one flow cell. when looking at the fastqc results of the samples, they all look strange. ![enter image description here][2] ![enter image description here][1] both overrepresented adapter and adapter content are in the green and sow no a ...
gc content peaks chip-seq fastqc written 2 days ago by Assa Yeroslaviz1.2k
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Comment: C: Find transcription factors that may regulate list of genes
... Enigma was last updated in 2008. I would suggest using it. ...
written 14 days ago by Assa Yeroslaviz1.2k
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Comment: C: high duplication levels in R1 reads of 10x Genomics samples
... of course I can. image R1 is below the text **R1**, image R2 is below the text **R2**. ...
written 23 days ago by Assa Yeroslaviz1.2k
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Comment: C: high duplication levels in R1 reads of 10x Genomics samples
... I did, and now? I don't know what you mean. ...
written 23 days ago by Assa Yeroslaviz1.2k
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high duplication levels in R1 reads of 10x Genomics samples
... Hi, I'm not sure if there is a reason to worry, but i would like to try and understand the problem. we have a 10x Genomics run sequenced in a nextSeq 500. I know that during the sequencing there can be duplications, but for the first time, we're now seeing that in the R1 reads, so basically, where ...
10x duplication rna-seq fastqc written 23 days ago by Assa Yeroslaviz1.2k • updated 23 days ago by i.sudbery4.1k
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Comment: C: Identification of the sequence insertion site in the genome
... I know this post is already vey old, but can you pls point to me where i can find out how to identify clipped reads using pysam. I can't find it in the docs. ...
written 5 weeks ago by Assa Yeroslaviz1.2k
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Comment: C: can delly identify multiple copies of a unique deletion?
... thanks for the explanation, but this was not my question. I am not interested in the biology behind it. I would like to know if, when using the tool **delly** for quantifying breakpoints, the problematic of having the same molecules multiple times is accounted for. Can delly quantify the number of ...
written 5 weeks ago by Assa Yeroslaviz1.2k
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can delly identify multiple copies of a unique deletion?
... Let's say we have the following situation. We have a unique breakpoint in mtDNA (a deletion in the mtDNA). If by chance this molecule is replicated and now this unique molecule exist as multiple copies. How would delly handle this situation? Can it distungish how many molecules exits in the sample ...
delly cnv written 6 weeks ago by Assa Yeroslaviz1.2k • updated 6 weeks ago by Vitis2.0k

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