User: Assa Yeroslaviz

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Assa Yeroslaviz1.4k
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Location:
Munich
Website:
https://www.biochem.mp...
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AssaYeroslaviz
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Last seen:
1 month, 1 week ago
Joined:
9 years, 6 months ago
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y*********@biochem.mpg.de

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 • 476 results • page 1 of 48 • next >
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Comment: C: How can I annotate multiple blast results?
... Yes, this is true, but we have to work with what we got. And I got stuck with the `gi` numbers :-( So I need to make the best out of it. I don't think `magicblast` can output something else. But thanks for the help. ...
written 5 weeks ago by Assa Yeroslaviz1.4k
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Comment: C: How can I annotate multiple blast results?
... Hi again, I'm not sure what `elink` should do, but with it in the command I don't get any results. $ esearch -db nuccore -query 34809228 | elink -target gene | esummary | xtract -pattern DocumentSummary -element Id,Caption,Organism Here I get no results, but with this $ esearch -db nuc ...
written 5 weeks ago by Assa Yeroslaviz1.4k
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Comment: C: How can I annotate multiple blast results?
... thanks, I was just now looking into `efetch` and `esearch` and tried to concatenate a pipeline for that. but you beat me to it. Thnaks again ...
written 5 weeks ago by Assa Yeroslaviz1.4k
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Comment: C: How can I annotate multiple blast results?
... I know I can't get it via `magicblast`. My question is how I can get it otherwise. ...
written 5 weeks ago by Assa Yeroslaviz1.4k
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Comment: C: How can I annotate multiple blast results?
... Yes, I would like to get the gene name and organism. ...
written 5 weeks ago by Assa Yeroslaviz1.4k
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How can I annotate multiple blast results?
... Hi, I have a list of hits from a `magicblast` run against a fastq file I have. I was wondering if there is a way to annotate the hits I get. The run was done against `nt` DB. The list of hits looks like that: NB500982:283:HH3WJAFX2:1:21210:15709:8224 gi|1040217674 100 0 0 0 1... NB500982: ...
annotation blast written 5 weeks ago by Assa Yeroslaviz1.4k • updated 5 weeks ago by GenoMax94k
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How to annotate a bam file?
... Hi, I'm looking for a method/tool for annotating a bam file. After running the mapping with STAR, I have filtered my bam file for specific reads, I am interested in. I would now like to assign a gene (nearest gene) or any other genomic structure, if possible to each of the reads. Best case scena ...
bam annotations written 8 weeks ago by Assa Yeroslaviz1.4k
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Comment: C: ggplot2 scater plot with three grouping parameters
... thanks, that with the `color` and `fill`options is a good solution ...
written 9 weeks ago by Assa Yeroslaviz1.4k
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ggplot2 scater plot with three grouping parameters
... Hi, I'm analyzing an RNA-Seq data set using DESeq2. While doing exploratory data analysis, I would like to plot a PCA of my data. In the PCA I would like to create three different grouping parameters - time, group and a third parameter called "with/without" ( an addition of a specific aggregate to ...
pca ggplot2 aes written 9 weeks ago by Assa Yeroslaviz1.4k
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Answer: A: bcftools mpileup create an empty output file
... ok, the problem was using the wrong threads parameter. Somehow I assumed that the threads number can be called with `-t`. But unfortunately this is a region parameter, and as such for a chromosome I don't have in my data set (as I have I,II,III, etc) so calling it correctly would be bcftools ...
written 10 weeks ago by Assa Yeroslaviz1.4k

Latest awards to Assa Yeroslaviz

Scholar 10 weeks ago, created an answer that has been accepted. For A: Approximate matching to find similar DNA sequence
Scholar 10 weeks ago, created an answer that has been accepted. For A: Approximate matching to find similar DNA sequence
Popular Question 3 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 4 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 4 months ago, created a question with more than 1,000 views. For fastqc Exception in thread "Thread-1" (error)
Popular Question 4 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 4 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 5 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Appreciated 5 months ago, created a post with more than 5 votes. For following Kallisto with DESeq2 using tximport package
Scholar 5 months ago, created an answer that has been accepted. For A: Approximate matching to find similar DNA sequence
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Saving A Table In R With Its Own Name
Student 5 months ago, asked a question with at least 3 up-votes. For following Kallisto with DESeq2 using tximport package
Popular Question 5 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Great Question 8 months ago, created a question with more than 5,000 views. For estimation of size factors in DESeq2 analysis
Popular Question 10 months ago, created a question with more than 1,000 views. For fastqc Exception in thread "Thread-1" (error)
Popular Question 10 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 10 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Great Question 11 months ago, created a question with more than 5,000 views. For estimation of size factors in DESeq2 analysis
Popular Question 14 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 15 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Great Question 15 months ago, created a question with more than 5,000 views. For estimation of size factors in DESeq2 analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object

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