User: reza

gravatar for reza
reza210
Reputation:
210
Status:
Trusted
Location:
Iran
Last seen:
3 weeks ago
Joined:
3 years, 4 months ago
Email:
r********@gmail.com

i am here to learn

Posts by reza

<prev • 107 results • page 1 of 11 • next >
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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 5 weeks ago by reza210
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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 3 months ago by reza210
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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 4 months ago by reza210
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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 4 months ago by reza210
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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 4 months ago by reza210
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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 7 months ago by reza210 • updated 7 months ago by harishk020170
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Comment: C: variant calling in mitochondria using whole genome sequencing
... when i set -ploidy 100, numbers of identified SNPs increased from 23 to 593 ! without apply of -ploidy on 100, my results (23 SNPs) are correct? ...
written 11 months ago by reza210
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variant calling in mitochondria using whole genome sequencing
... i performed variant calling in mitochondria using whole genome sequencing data by GATK UnifiedGenotyper. Genotype of some SNPs specially those are in D-loop region is heterozygote (0/1). Is it due to heteroplasmy? ...
mitochondria snp written 11 months ago by reza210
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Comment: C: several effect for one SNP annotated by SNPeff
... i did it, i described it in my question ...
written 11 months ago by reza210
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Comment: C: several effect for one SNP annotated by SNPeff
... i have vcf file resulted from standard workflow of variant calling (fastq files mapped to reference genome, post-alignment steps, variant calling by samtools). under study species is Bactrian camel ...
written 12 months ago by reza210

Latest awards to reza

Popular Question 3 months ago, created a question with more than 1,000 views. For CLC worcbench assembly
Popular Question 3 months ago, created a question with more than 1,000 views. For CLC worcbench assembly
Popular Question 7 months ago, created a question with more than 1,000 views. For CLC worcbench assembly
Popular Question 7 months ago, created a question with more than 1,000 views. For CNV detection using BAM file
Popular Question 7 months ago, created a question with more than 1,000 views. For SNP annotation in non model animals
Popular Question 7 months ago, created a question with more than 1,000 views. For cygwin error when i try to install platypus (variant caller)
Popular Question 7 months ago, created a question with more than 1,000 views. For segmentation fault (core dumped) error when using BWA and BOWTIE
Popular Question 7 months ago, created a question with more than 1,000 views. For how to select longest isoform per gene in gtf
Popular Question 7 months ago, created a question with more than 1,000 views. For Augustus running error
Popular Question 9 months ago, created a question with more than 1,000 views. For CLC worcbench assembly
Popular Question 9 months ago, created a question with more than 1,000 views. For Augustus running error
Popular Question 9 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 10 months ago, created a question with more than 1,000 views. For cygwin error when i try to install platypus (variant caller)
Popular Question 10 months ago, created a question with more than 1,000 views. For Augustus running error
Centurion 12 months ago, created 100 posts.
Popular Question 13 months ago, created a question with more than 1,000 views. For variant calling after mapping via bwa mem
Popular Question 13 months ago, created a question with more than 1,000 views. For cygwin error when i try to install platypus (variant caller)
Popular Question 13 months ago, created a question with more than 1,000 views. For how to select longest isoform per gene in gtf
Popular Question 15 months ago, created a question with more than 1,000 views. For variant calling after mapping via bwa mem
Popular Question 19 months ago, created a question with more than 1,000 views. For building database in snpEff
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 21 months ago, created a question with more than 1,000 views. For building database in snpEff
Popular Question 22 months ago, created a question with more than 1,000 views. For building database in snpEff
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Problems with Trimmomatic PE output files

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