User: reza
reza • 220
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- 2 weeks, 6 days ago
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- 3 years, 8 months ago
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i am here to learn
Posts by reza
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... Yes, this command is vdb-config -i (command for opening configuration window) actually. after configuration, this message will be repeated again and again ...
written 5 weeks ago by
reza • 220
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... 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 ...
written 5 weeks ago by
reza • 220
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... 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 4 months ago by
reza • 220
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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 7 months ago by
reza • 220
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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 7 months ago by
reza • 220
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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 7 months ago by
reza • 220
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... 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 ...
written 7 months ago by
reza • 220
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... 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? ...
written 11 months ago by
reza • 220
• updated
11 months ago by
harishk0201 • 70
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... 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 15 months ago by
reza • 220
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... 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? ...
written 15 months ago by
reza • 220
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