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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3 days, 2 hours ago
Joined:
7 years, 6 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 • 326 results • page 1 of 33 • next >
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combine shRNA-Seq on gene level
... Hi, I have a dataset of shRNA-Seq library with multiple shRNA for many different genes. I have done the analysi on each of the 187 shRNA molecules. Now i would like to combine the analysis on the gene level. Is it possible, just to merge the results for all of the shRNA molecules of each gene, by c ...
ngs shrna-seq limma roast written 5 weeks ago by Assa Yeroslaviz1.1k
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calculating extinction coefficient for thousands of peptides
... I'm looking for a tool to calculated peptide properties, especially extinction coefficient of a peptide. I have a very long list of various peptides and I would to automate the process. Does anyone know of a tool for offline use? or programmatically? thanks ...
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Comment: C: unmapped reads in paired-end run pf bowtie2
... thanks, I'll look into it ...
written 6 months ago by Assa Yeroslaviz1.1k
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Comment: C: unmapped reads in paired-end run pf bowtie2
... I thought so too. But if I use the same command but with `--un-gz` and the input files `-1 1.fq.gz -2 2.fq.gz`, the unmapped file is empty. Is there a way to map the files in a paired-end modus and still get the unmapped **reads**, not pairs? ...
written 6 months ago by Assa Yeroslaviz1.1k
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Comment: C: unmapped reads in paired-end run pf bowtie2
... Just to add - this is the output of the same file when running the `samtools flagstat` command ``` 7206695 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 7206695 + 0 mapped (100.00% : N/A) 7206695 + 0 paired in sequencing 3615165 + 0 read1 3591 ...
written 6 months ago by Assa Yeroslaviz1.1k
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Comment: C: unmapped reads in paired-end run pf bowtie2
... This is the commands i use ``` bowtie2 --sensitive --end-to-end -p 10 --un-conc-gz firstRun.Unmapped.gz --phred33 -x genome -1 1.fq.gz -2 2.fq.gz | samtools view -Sbhu -F 4 - | samtools sort - -o sorted.bam samtools index sorted.bam ``` The file I need in the next step is `firstRun.Unmapped.gz`. ...
written 6 months ago by Assa Yeroslaviz1.1k
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unmapped reads in paired-end run pf bowtie2
... I have a data set of paired-end samples which I'm mapping with bowtie2. I am mainly focus on the unmapped reads, as these are the reads we're interested in. This is a sample output of the mapping results from on of my runs: 11216394 reads; of these: 11216394 (100.00%) were paired; of thes ...
paired-end bowtie unmapped-reads written 6 months ago by Assa Yeroslaviz1.1k • updated 6 months ago by Devon Ryan87k
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Comment: C: BioMart dataset for S pombe
... > makeTxDbFromBiomart(biomart ="fungal_mart" ,dataset="spombe_eg_gene" ,host="fungi.ensembl.org") This would work with the correct name makeTxDbFromBiomart(biomart ="fungi_mart" ,dataset="spombe_eg_gene" ,host="fungi.ensembl.org") ...
written 7 months ago by Assa Yeroslaviz1.1k
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Comment: C: extracting orphan reads from bam file
... What's the point of giving a standard reply, if you're not willing to help understanding the answer you give? I have tried to understand your tool and the comments in the linked answer, but I am not sure if this is the correct method. I would appreciate further help. ...
written 7 months ago by Assa Yeroslaviz1.1k
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Comment: C: detecting insertion sites of transgene in mouse genome
... Do you have any ideas how to increase the number of mapped reads to the ends of the transgene sequence when using bwa as a mapper? I have read the manual, but not sure how to decrease the sensitivity. thanks ...
written 7 months ago by Assa Yeroslaviz1.1k

Latest awards to Assa Yeroslaviz

Student 5 weeks ago, asked a question with at least 3 up-votes. For estimation of size factors in DESeq2 analysis
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Popular Question 7 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 8 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
Popular Question 10 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Student 10 months ago, asked a question with at least 3 up-votes. For estimation of size factors in DESeq2 analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Popular Question 13 months ago, created a question with more than 1,000 views. For fastqc Exception in thread "Thread-1" (error)
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Great Question 16 months ago, created a question with more than 5,000 views. For Go Enrichment Of Rna-Seq Data
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Popular Question 18 months ago, created a question with more than 1,000 views. For HOWTO extract regions from GRanges object
Good Question 18 months ago, asked a question that was upvoted at least 5 times. For following Kallisto with DESeq2 using tximport package
Prophet 18 months ago, created a post with more than 20 followers. For The Difference Between Directional And Nondirectional Sequencing

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