User: grant.hovhannisyan

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Posts by grant.hovhannisyan

<prev • 334 results • page 1 of 34 • next >
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Comment: C: normalization with RPKM
... No, its a standalone software. Here is the link https://ccb.jhu.edu/software/stringtie/ ...
written 10 days ago by grant.hovhannisyan1.5k
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Comment: C: normalization with RPKM
... RPKM/FPKM is a unit, not a method or analysis. Today, people usually use TPM unit instead of R(F)PKM. To calculate TPM, you can run your bam files through Stringtie software, or you can use Salmon or Kallisto software using the fastq files directly. ...
written 10 days ago by grant.hovhannisyan1.5k
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Answer: A: Dual rnaseq normalization
... If you have successfully separated the reads of the host and pathogen, and have the count table for each species, then you can proceed with a standard DESeq2 analysis. If you have time-series design, you should follow the instruction in DESeq2 vignette https://www.bioconductor.org/packages/devel/bio ...
written 9 weeks ago by grant.hovhannisyan1.5k
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Comment: C: Bwa Mem Have Different Alignment Result When Using Different Threads
... I would say that this epsilon should really depend on the area of research, while for experimental biology of course nothing can be 100% reproducible, for bioinofrmatics part I guess it should be really close to 0. Also depends on what is the conclusion, if it is a number of open-chromatin peaks, so ...
written 9 weeks ago by grant.hovhannisyan1.5k
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Comment: C: Bwa Mem Have Different Alignment Result When Using Different Threads
... Sorry, I already rerun the pipeline with the number of cores I had before. But I work with a non-model yeast S. uvarum, here is the genome http://www.saccharomycessensustricto.org/cgi-bin/s3.cgi?data=Assemblies&version=current, so in general there are a lot of headaches with it :) ...
written 9 weeks ago by grant.hovhannisyan1.5k
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Comment: A: 10 Most important topic in Human evolutionary genomics
... One very hot topic in human evolutionary genomics is ancient DNA studies and how they transformed our views in human evolution. There are plenty of recent high profiles papers on this topic. Also you can maybe talk about cultural traits like language, lifestyle (agriculturalism, hunting-gathering, ...
written 9 weeks ago by grant.hovhannisyan1.5k
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Comment: C: Bwa Mem Have Different Alignment Result When Using Different Threads
... Well, something is either reproducible or not, and in this case BWA is one of the most used software in bioinformatics, that's why I say quite big. Imagine how much time in total the community would spend to figure out what is wrong in a large pipeline, which produces slightly different results. An ...
written 9 weeks ago by grant.hovhannisyan1.5k
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Answer: A: Bwa Mem Have Different Alignment Result When Using Different Threads
... I have to say that after several years, this issue still persists, which I think is a quite big reproducibility issue. Especially when the pipeline consists of many steps, the inconsistencies accumulate on top of each other like a snowball. I use version 0.7.17-r1188 bwa mem -t 10 SC_masked 4 ...
written 9 weeks ago by grant.hovhannisyan1.5k
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Comment: C: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
... +1 For Michael Love. The developer of STAR, Alex Dobin, is from the same brilliant category of Bioinformaticians. ...
written 10 weeks ago by grant.hovhannisyan1.5k
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Comment: C: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
... I'd suggest to classify by disciplines. For many people here Bioinformatics is usually related to NGS, but there are also phylogenetics, population genetics, structural biology, etc which were "Bioinformatics" long before NGS. ...
written 10 weeks ago by grant.hovhannisyan1.5k

Latest awards to grant.hovhannisyan

Popular Question 15 days ago, created a question with more than 1,000 views. For Display pairwise p values on barplots in ggplot2
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Scholar 12 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
Popular Question 3 months ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
Popular Question 5 months ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
Appreciated 6 months ago, created a post with more than 5 votes. For Technical replicates in RNAseq
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Technical replicates in RNAseq
Popular Question 6 months ago, created a question with more than 1,000 views. For Read counts of STAR with gff file
Popular Question 6 months ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
Scholar 7 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Popular Question 8 months ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
Scholar 8 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Scholar 8 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Scholar 9 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Guru 10 months ago, received more than 100 upvotes.
Student 10 months ago, asked a question with at least 3 up-votes. For Technical replicates in RNAseq
Popular Question 11 months ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
Scholar 12 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Popular Question 13 months ago, created a question with more than 1,000 views. For Read counts of STAR with gff file
Scholar 15 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO

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