User: reza

gravatar for reza
reza230
Reputation:
230
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Trusted
Location:
Iran
Last seen:
3 months, 2 weeks ago
Joined:
4 years, 4 months ago
Email:
r********@gmail.com

i am here to learn

Posts by reza

<prev • 111 results • page 1 of 12 • next >
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Meta-Analysis of Microarray data (Afyymetrix)
... Hi everyone I am doing a meta-analysis of microarray data (AffyMetrix; 4 sets). Normalization by RMA using the “Afyy” package in R and extraction of normalized data was done. >rawdata<-ReadAffy() >PM<-probes(rawdata,which="pm") >AffyInfo&l ...
R meta-analysis affymetrix microarray written 4 months ago by reza230
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extraction of scaffolds from SOAPdenovo output
... hi everyone I did a denovo-assembly using soapdenove, now the output of soap, tell me that I have 1744860 singletons and 95021 scaffolds. I want to extract scaffolds from the output file. anybody can help me to do that? ...
assembly next-gen soapdenovo scaffold written 5 months ago by reza230
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Comment: C: A problem with download SRA using SRA toolkit
... Yes, this command is vdb-config -i (command for opening configuration window) actually. after configuration, this message will be repeated again and again ...
written 9 months ago by reza230
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A problem with download SRA using SRA toolkit
... I want to download the SRA using SRA toolkit, so I installed it using this guidance: https://github.com/ncbi/sra-tools/wiki/Building-and-Installing-from-Source and then configured it using this guidance: https://github.com/ncbi/sra-tools/wiki/05.-Toolkit-Configuration but when I used below comma ...
ncbi sra sra toolkit configuration written 9 months ago by reza230 • updated 3 months ago by eynardrenaud0
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Comment: C: Multiple genome comparison for new genetic markers
... There are so many resources that can help you in this field; You just have to do a simple search in Google. like this: [Variant Calling Pipeline: FastQ to Annotated SNPs in Hours][1] [1]: https://gencore.bio.nyu.edu/variant-calling-pipeline/ ...
written 13 months ago by reza230
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Comment: C: Issue with Bowtie2 mapping
... Thank you for trying to help me. i have no problem with reads number. Program in each run, show different behaviors, which I think is due to the existence of a bug. ...
written 15 months ago by reza230
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Comment: C: Issue with Bowtie2 mapping
... Based on FastQC report, each cleaned files (for. and rev.) have 201720569 but Bowtie2 used 98031099 reads to mapping ...
written 16 months ago by reza230
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Comment: C: Issue with Bowtie2 mapping
... i used clean reads to reference mapping, discarded reads by Trimmomatic deposited into D1R1U.fastq and D1R2U.fastq and were ignored from downstream acts. ...
written 16 months ago by reza230
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Issue with Bowtie2 mapping
... I am working on a sets of paired end reads, in first step I trimmed them using Trimmomatic with following command java -jar trimmomatic-0.36.jar PE 10.10B_R1.gz 10.10B_R2.gz D1R1P.fastq D1R1U.fastq D1R2P.fastq D1R2U.fastq LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50 There are 201720569 re ...
trimmomatic bowtie2 paired-end mapping written 16 months ago by reza230
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whole genome alignment using nucmer
... hi i aligned two whole genome using nucmer with this simple command nucmer reference_genome.fasta query_genome.fasta then three outputs files were created: out.delta, out.coordinates, out.tiling Now, is there any way to know how percent of reference genome, covered by query genome? ...
genome assembly alignment nucmer written 19 months ago by reza230 • updated 19 months ago by harishk020170

Latest awards to reza

Popular Question 10 months ago, created a question with more than 1,000 views. For CLC worcbench assembly
Popular Question 10 months ago, created a question with more than 1,000 views. For installing ABYSS using cygwin
Popular Question 15 months ago, created a question with more than 1,000 views. For CLC worcbench assembly
Popular Question 15 months ago, created a question with more than 1,000 views. For CLC worcbench assembly
Popular Question 19 months ago, created a question with more than 1,000 views. For CLC worcbench assembly
Popular Question 19 months ago, created a question with more than 1,000 views. For CNV detection using BAM file
Popular Question 19 months ago, created a question with more than 1,000 views. For SNP annotation in non model animals
Popular Question 19 months ago, created a question with more than 1,000 views. For cygwin error when i try to install platypus (variant caller)
Popular Question 19 months ago, created a question with more than 1,000 views. For segmentation fault (core dumped) error when using BWA and BOWTIE
Popular Question 19 months ago, created a question with more than 1,000 views. For how to select longest isoform per gene in gtf
Popular Question 19 months ago, created a question with more than 1,000 views. For Augustus running error
Popular Question 21 months ago, created a question with more than 1,000 views. For CLC worcbench assembly
Popular Question 21 months ago, created a question with more than 1,000 views. For Augustus running error
Popular Question 21 months ago, created a question with more than 1,000 views. For workflow for variant calling using GATK in multiple paired end reads
Popular Question 22 months ago, created a question with more than 1,000 views. For cygwin error when i try to install platypus (variant caller)
Popular Question 22 months ago, created a question with more than 1,000 views. For Augustus running error
Centurion 23 months ago, created 100 posts.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For variant calling after mapping via bwa mem
Popular Question 2.1 years ago, created a question with more than 1,000 views. For cygwin error when i try to install platypus (variant caller)
Popular Question 2.1 years ago, created a question with more than 1,000 views. For how to select longest isoform per gene in gtf
Popular Question 2.2 years ago, created a question with more than 1,000 views. For variant calling after mapping via bwa mem
Popular Question 2.6 years ago, created a question with more than 1,000 views. For building database in snpEff
Popular Question 2.6 years ago, created a question with more than 1,000 views. For how to select longest isoform per gene in gtf
Popular Question 2.7 years ago, created a question with more than 1,000 views. For building database in snpEff

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