User: reza
reza • 210
- 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 >
0
votes
0
answers
60
views
0
answers
... 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
reza • 210
0
votes
0
answers
223
views
0
answers
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
reza • 210
0
votes
0
answers
223
views
0
answers
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
reza • 210
0
votes
0
answers
223
views
0
answers
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
reza • 210
0
votes
0
answers
223
views
0
answers
... 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 4 months ago by
reza • 210
4
votes
2
answers
364
views
2
answers
... 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 7 months ago by
reza • 210
• updated
7 months ago by
harishk0201 • 70
0
votes
0
answers
432
views
0
answers
... 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
reza • 210
1
vote
0
answers
432
views
0
answers
... 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 11 months ago by
reza • 210
0
votes
1
answer
523
views
1
answers
... i did it, i described it in my question ...
written 11 months ago by
reza • 210
0
votes
1
answer
523
views
1
answers
... 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
reza • 210
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 how to extract gene name for non-synonymous SNPs from annotated vcf file for GO analysis
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 770 users visited in the last hour