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 • 379 results • page 1 of 38 • next >
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Comment: C: how to index different genomes with snakemake with different parameters?
... I don't know what happened, I thought I have got it, but it seems to be not working anymore. This is how my `config.yaml` file look like organism: Dmel: fasta: "ftp://ftp.ensembl.org/pub/current_fasta/drosophila_melanogaster/dna/Drosophila_melanogaster.BDGP6.22.dna.toplevel.fa.gz ...
written 1 day ago by Assa Yeroslaviz1.2k
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Comment: C: how to index different genomes with snakemake with different parameters?
... thanks for this great example. I will try it immediately. I was just wondering what you mean in the `run` comment. Something in the way adding a list in the config file like: organism: ["GRCh38", "GRCm38", "BDGP6.22"] But where does snakemake know how to get the link for each of the ...
written 14 days ago by Assa Yeroslaviz1.2k
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how to index different genomes with snakemake with different parameters?
... I would like to use snakemake to analyze my data sets. As I am going to work with different organisms, I would like snakemake to create a folder for each of them when indexing the genome. let's say I would like to work with human and mouse data. In my `config.yaml` file I have the following snippe ...
indexing snakemake mapping written 14 days ago by Assa Yeroslaviz1.2k • updated 14 days ago by Eric Lim1.6k
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Comment: C: problem with missing input file in snakemake rule
... I'm not sure how else I can do that. How can I call for a rule with wildcards in the output? e.g. How can I run the `rule index` by itself? ...
written 5 weeks ago by Assa Yeroslaviz1.2k
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Comment: C: problem with missing input file in snakemake rule
... yes, this worked fine. Thanks for that. I still don't understand this kind of error though. I have added another rule now for the quantification using featureCounts. rule quant: input: gtf = "data/genome.gtf", bam = expand("Analysis/star/bamFiles/{sample}.bam", ...
written 5 weeks ago by Assa Yeroslaviz1.2k
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Comment: C: problem with missing input file in snakemake rule
... This make sense. I'll try it. thanks ...
written 5 weeks ago by Assa Yeroslaviz1.2k
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problem with missing input file in snakemake rule
... I'm trying to convert the `SJ.tab.out` file from STAR into a bed file within a snakemake script. the rule for that is this: rule map_star_SE: input: R1='data/samples/single-end/{sample}_R1.fastq', index=directory("data/starIndex/") output: b ...
snakemake rule star mapping written 6 weeks ago by Assa Yeroslaviz1.2k
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Comment: C: snakemake errors and threads
... thanks. i forgot to add it. ...
written 6 weeks ago by Assa Yeroslaviz1.2k
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snakemake errors and threads
... I'm trying to implement a snakemake workflow for my fastq files This is my rule for mapping: gz_command="--readFilesCommand zcat" if config["gzipped"] else "" # main snakefile configfile:"config.yaml" SAMPLES=["1_S1", "2_S2", "3_S3", "4_S4"] rule all: input: ...
threads snakemake align star written 6 weeks ago by Assa Yeroslaviz1.2k
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Setting the experimental design in a germline translatome analysis
... I have a general question about an experiment we're planning. We would like to analyze how well various **germline** mRNA are being translated. For that we're planning to extract germline ribosome via Immunoprecipitation specifically for germline ribosomes. For that i have two question. The first ...
translation profiling trap-seq ribo-seq written 7 weeks ago by Assa Yeroslaviz1.2k

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Popular Question 15 days ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
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Popular Question 3 months ago, created a question with more than 1,000 views. For fastqc Exception in thread "Thread-1" (error)
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