User: Assa Yeroslaviz

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Assa Yeroslaviz1.1k
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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 • 324 results • page 1 of 33 • next >
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Comment: C: unmapped reads in paired-end run pf bowtie2
... thanks, I'll look into it ...
written 7 weeks 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 7 weeks 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 7 weeks 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 7 weeks 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 7 weeks ago by Assa Yeroslaviz1.1k • updated 7 weeks ago by Devon Ryan82k
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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 9 weeks 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 10 weeks 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 11 weeks 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 12 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 3 months ago by Assa Yeroslaviz1.1k

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