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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6 years, 11 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 • 320 results • page 1 of 32 • next >
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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 20 hours ago by Assa Yeroslaviz1.1k
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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 11 days 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 18 days 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 28 days ago by Assa Yeroslaviz1.1k
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Comment: C: extracting orphan reads from bam file
... Thanks Pierre, I am not sure how to use this snippet to my needs. The bam file I have is the results of the combined indexed genome from mouse and transgene. How does it knows which chromosome belongs to mouse and (e.g. host) which to transgene (e.g. virus)? Do I need to change the script to someth ...
written 4 weeks ago by Assa Yeroslaviz1.1k
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extracting orphan reads from bam file
... Hi, I have a bam file from WGS sequencing, wehre I try to identify the integration site(s) of a transgene insertion in the mouse genome. I have run the mapping of the paired-end samples with bwa against the indexed transgene sequence. The goal was to identify those reads which were mapped with only ...
bam file samtools bwa orphan reads sa flag written 5 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: detecting insertion sites of transgene in mouse genome
... the paper mentioned in the answer - is there a way to get the workflow used here? Is it relevant only for targeted sequencing and TLA-prepared samples or can I re-use it also for "normal/standard" WGS experiment? ...
written 5 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: detecting insertion sites of transgene in mouse genome
... I am not really sure what happens after grepping the `SA:` reads. As you mentioned I visualize them in (e.g.) IGV, but what then? I guess it won't be a one-2-one situation, but probably multiple positions. How can I join the reads mapped to the transgene insert with their partners in a different ch ...
written 5 weeks ago by Assa Yeroslaviz1.1k
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Comment: C: detecting insertion sites of transgene in mouse genome
... Thanks a lot for the suggestion. how can i filter my bam files for the split reads? can `BWA` do soft-clipping? ...
written 8 weeks ago by Assa Yeroslaviz1.1k
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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 9 weeks ago by Assa Yeroslaviz1.1k

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