User: Assa Yeroslaviz

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Assa Yeroslaviz1.1k
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Munich
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http://www.biochem.mpg...
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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 • 311 results • page 1 of 32 • next >
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Comment: C: detecting insertion sites of transgene in mouse genome
... Tahnks for the fast answer. > Important questions : How many insertion sites did you expect ? I expect one or two sites, but it is a hypothesis, so there might be some more. > Important questions : What is the size of the foreign DNA ? What is the size of your reads ? The foreign DNA is ...
written 6 hours ago by Assa Yeroslaviz1.1k
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detecting insertion sites of transgene in mouse genome
... we have a pilot project consisting of one WGS paired-end sample from mouse. The mouse were inserted with a transgene of known sequence. We would like to identify possible insertion sites for this transgene. I was wondering which tool can help me do that. What I was thinking to do is to map the rea ...
transgene wgs insertion blast written 8 hours ago by Assa Yeroslaviz1.1k • updated 5 hours ago by Carambakaracho110
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How to analyse data from genetic screening followed by NGS ?
... Hi, We are planning on doing two genetic screening experiments, one is done with Crispr plasmids, the second one is done via gene-trapping retrovirus. Even though the methods are different, the idea behind the analysis should be similar. in both data sets after infecting the cells with wither the l ...
crispr grna gene-trapping screening de-analysis written 7 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: subset gtf file based on coordinates
... Thanks for the suggestion, but I think I am not doing it right. :-) I load the two files # load the gtf file gtf.gr <- import(con ="~/genomes/Caenorhabditis_elegans/Ensembl/WBcel235.2017/Annotation/Genes/genes.gtf", format = "gtf" ) gtf.gr <- sortSeqlevels(gtf.gr) # make sure it ...
written 9 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: subset gtf file based on coordinates
... this seems to work thanks ...
written 9 weeks ago by Assa Yeroslaviz1.1k
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has anyone ever worked with the CNCI tool
... Hi, Has anyone ever worked with the CNCI tool from [www-bioinfo-org (github)][1]. Iam trying to analyse my lncRNA data set with a self-made lncRNA-gtf file. but I get the following error when running the compare.py: $python /local/Assa/software/CNCI/compare.py -c ~/genomes/Caenorhabditis_ ...
cnci lncrna non-coding written 9 weeks ago by Assa Yeroslaviz1.1k • updated 28 days ago by Biostar ♦♦ 20
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subset gtf file based on coordinates
... Hi, I have a gtf file based on Ensembl chromosomes and gene IDs. I would like to extract the genes in it based on a second **bed** file. This Bed file though comes from a different source (lncRNA DB - www.noncode.org). I would like to extract all the genes from the gtf file which falls within the ...
gtf bed genomic ranges rna-seq subset written 9 weeks ago by Assa Yeroslaviz1.1k • updated 9 weeks ago by ATpoint3.5k
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Comment: C: DE analysis of lncRNA from C elegans
... In the "normal" DE analysis results I have done with the STAR-featureCounts-DESeq2 workflow I have also got some of linc* genes I was referring to. But all except one are not differentially expressed in the conditions i am working with. Now I am not sure, whether this is a biological result or it i ...
written 11 weeks ago by Assa Yeroslaviz1.1k
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DE analysis of lncRNA from C elegans
... Hi all, I was wondering how to do a differential expression analysis of long non-coding RNA (lncRNA) from my data set of C elegans samples. We have multiple samples from four different conditions. The raw data came from total-RNA. We have done already RNA-Seq analysis on the samples and woule like ...
deseq2 limma differential expression lncrna written 11 weeks ago by Assa Yeroslaviz1.1k • updated 11 weeks ago by swbarnes23.4k
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Comment: C: allelic specific expression with Kallisto
... I don't know what that is. ...
written 3 months ago by Assa Yeroslaviz1.1k

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