User: morovatunc

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morovatunc360
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360
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Turkey
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mortunco
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1 month ago
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3 years ago
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Posts by morovatunc

<prev • 185 results • page 1 of 19 • next >
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Comment: C: Does anybody success to download data using icgc-storage-client ?
... I think you should write to ICGC help desk. They are very helpful. Also I suggest you to log in to the spesific ec2 region. As far as I know, USA ec2 servers have access to icgc data. Final thing, make sure you set your key code. (The code that lets you access to the restricted data.) ...
written 11 weeks ago by morovatunc360
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Comment: C: Starrseq data how can I characterise reads that maps out of the targeted regions
... Yeah. I think it is cap-starrseq because I remember the preparation of the array design, forward and reverse primers etc. (Sorry for my ignorance, I mainly focus on the computational part of this project.) Could you help me to understand why you are not very concerned with %70 unspecific mappings?( ...
written 12 weeks ago by morovatunc360
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Comment: C: Starrseq data how can I characterise reads that maps out of the targeted regions
... qualimap is highly appreciated. I have been using it for 3 weeks in multiple projects. ...
written 12 weeks ago by morovatunc360
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Starrseq data how can I characterise reads that maps out of the targeted regions.
... Hi, We conducted starrseq experiment that measures the actives of the given library. (Say enhancers). Then, we send this data to WGS. **Background:** Mapping: We have ~250million reads with 150 bp paired end data. We used bowtie with -v 3 -m 1 —best —strata -X 2000 parameters. Then we analysed ...
starrseq alignment mapping sequencing written 3 months ago by morovatunc360
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Comment: C: Simplest output format of blast contamination check
... Yeah yeah you are totally right about the precaution beforehand. Currently, I am just doing this to check to find the most obvious ones. I dont want to mess with the default word size and mismatch levels. Is there way that I can make this tuning simpler? ...
written 5 months ago by morovatunc360
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Comment: C: Simplest output format of blast contamination check
... For the runs please see the reply on top. I have taken a look to blobtools paper. It seems to mine output of blast to make the graphs actually. blastn -outfmt "6 qseqid staxids bitscore std" -query kefal.contigs.fasta -db /mnt/compgen/inhouse/share/blastdb/nt -o kefal_canu_megablast.out ( th ...
written 5 months ago by morovatunc360
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Comment: C: Simplest output format of blast contamination check
... The assembly is ~900 MB size (in fasta). The length is .9 Gbps. I tried; megablast -i kefal.contigs.fasta -d /mnt/compgen/inhouse/share/blastdb/nt -o kefal_canu_megablast.out blastn -i kefal.contigs.fasta -d /mnt/compgen/inhouse/share/blastdb/nt -o kefal_canu_megablast.out ...
written 5 months ago by morovatunc360
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Simplest output format of blast contamination check
... Dear all hi, I have finalsed a de-novo assembly of a uncharacterised organism. To be able to check bacteria etc contamination we would like to use blast NT library. When I try blast with default settings, I simply get 33Gb of data which I dont need it. My aim is to get single percentage output su ...
megablast blast written 5 months ago by morovatunc360 • updated 5 months ago by h.mon16k
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Comment: C: Sub-typing patients by a single gene's expression in TCGA dataset.
... Yes. You are exactly right. Those samples are all spesified as Tumor. But I am trying to separate them based on the expression of a given gene (say X). I havent thought about exploring the distribution and the GTEX thing. Thank you very much for reminding that ! I will give this method a try. ...
written 5 months ago by morovatunc360
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Sub-typing patients by a single gene's expression in TCGA dataset.
... Hi, We have experimentally found that given gene X causes some phenotype. To start exploring the underlying mechanism, we decided to use TCGA data as its freely available. So within the cancer patients can we simple divide two samples based on gene X expression. The first thing that came to my min ...
tcga rna-seq written 5 months ago by morovatunc360 • updated 5 months ago by Michele Busby1.8k

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