User: reza
reza • 230
- Reputation:
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- Iran
- Last seen:
- 3 months, 2 weeks ago
- Joined:
- 4 years, 4 months ago
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i am here to learn
Posts by reza
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... 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 ...
written 4 months ago by
reza • 230
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... 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? ...
written 5 months ago by
reza • 230
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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 9 months ago by
reza • 230
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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 9 months ago by
reza • 230
• updated
3 months ago by
eynardrenaud • 0
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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 13 months ago by
reza • 230
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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
reza • 230
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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
reza • 230
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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
reza • 230
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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 16 months ago by
reza • 230
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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 19 months ago by
reza • 230
• updated
19 months ago by
harishk0201 • 70
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