User: morovatunc

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morovatunc360
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Turkey
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mortunco
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an hour ago
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Posts by morovatunc

<prev • 181 results • page 1 of 19 • next >
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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 4 days 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 4 days 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 4 days 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 4 days ago by morovatunc360 • updated 4 days ago by h.mon11k
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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 15 days 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 18 days ago by morovatunc360 • updated 16 days 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 19 days 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 27 days 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 5 weeks ago by morovatunc360
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Comment: C: Extract Cg Dinucleotides Coordinates From (Human) Genome
... I dont know if it useful or not but I used your script and it is running. Thank you. I have a question; What is the format that you got at the end of it. I had to put "End" manually but when I compared your chr,Start file format vs mine(chr start end gave the same thing. Thanks. ...
written 8 months ago by morovatunc360

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
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 4 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
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Popular Question 8 months ago, created a question with more than 1,000 views. For Chip-Seq Peak hight difference between BED and BW file formats.
Popular Question 11 months ago, created a question with more than 1,000 views. For HOMER find motifs from BED data
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