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 day, 14 hours ago
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2 years, 9 months ago
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Posts by morovatunc

<prev • 182 results • page 1 of 19 • next >
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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 2 days 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 8 weeks 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 8 weeks 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 8 weeks 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 8 weeks ago by morovatunc360 • updated 8 weeks ago by h.mon13k
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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 10 weeks 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 10 weeks ago by morovatunc360 • updated 10 weeks ago by Michele Busby1.7k
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Designed primers with 3 bp mutations (codons) how to validate/visualize them?
... Dear all hi, I was given a sequence of 1500 bps. I was asked to replace each amino acid with the rest 19 based on codon usage in human. To control what I have done, I tried to map them with bwa to my subject region and used blastn for the local alignment but for some regions i did not work. my pr ...
blast bwa primer written 11 weeks ago by morovatunc360
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Answer: A: detecting mutations in cancer samples belonging to the same cancer type
... There are mutation callers for this purpose. Depending on your sample you may want to use more than one or taking the intersections. (Algorithms have pros and cons for different sample types). https://github.com/Illumina/strelka http://dkoboldt.github.io/varscan/ https://software.broadinstitute.o ...
written 12 weeks ago by morovatunc360
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BWA aligner parameter tweaking to show primer mapping
... Hi guys, I generated some primers by mutating amino acids in a DNA sequence of 1553 bases.. My primer structure is as follows; > 19bp sequence(flanking sequence%100 match)+ 3 bp (mutated) + 19 > bpsequence(flanking sequence %100 match) Say i have some sequence that start with start codon. F ...
primer-design bwa written 3 months ago by morovatunc360

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Popular Question 7 days ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
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Popular Question 3 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
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Popular Question 5 months ago, created a question with more than 1,000 views. For Finding Chip Seq Overlaps with Bed files
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Popular Question 12 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
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