User: grant.hovhannisyan

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Posts by grant.hovhannisyan

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Comment: C: Low mapping rate for human NGS PE reads to hs37d5 genome
... I would say 88% is not actually very low, but within acceptable limits, we usually get 85-95%. But anyway, you also might try to run FASTQC on your raw data to see if you have any adapters or overrepresented sequences. ...
written 1 day ago by grant.hovhannisyan1.7k
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Comment: C: NGS data analysis training
... If you tell us what specifically you want to analyze, we can be more helpful in giving you advices. ...
written 1 day ago by grant.hovhannisyan1.7k
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Comment: C: Heterozygous genome size estimation using k-mer analysis
... not an answer to your question, but you might (heavily) overestimate the size of the heterozygous genome if you assemble it with usual pipelines, because they might assemble heterozygous regions into separate scaffolds. The pipeline above takes this into accounts and also provides some useful metric ...
written 19 days ago by grant.hovhannisyan1.7k
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Answer: A: Heterozygous genome size estimation using k-mer analysis
... look here https://www.ncbi.nlm.nih.gov/pubmed/27131372 ...
written 19 days ago by grant.hovhannisyan1.7k
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Answer: A: Genome vs transcriptome alignement in STAR
... If you used `--quantMode GeneCounts`, then in count file there will be `N_noFeature`, i.e. reads that were not assigned to any feature. It can be a proxy of how much "genomic" reads you have. However if you work a non-model organism it can be that these reads are coming from not yet annotated genes ...
written 23 days ago by grant.hovhannisyan1.7k
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Answer: A: Is it possible to detect lncRNA in a de novo assembled genome?
... No problem, just assemble the transcripts and then assess their coding potentials. Would be good to use several tools for coding potential and then see if their results overlap. ...
written 4 weeks ago by grant.hovhannisyan1.7k
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Comment: C: Atypical Volcano plot of RNAseq data
... What is your organism? Are you sure you did not apply any filtering on fold-change? Basically you have a set of (I bet lowly expressed, or probably even co-expressed) genes which have a really big fold change. You can filter your data with p-val and and fold-change to see what are these outliers, ma ...
written 4 weeks ago by grant.hovhannisyan1.7k
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Comment: C: Why I have too many reads non uniquely aligned?
... For dif. gene expression analysis (I assume you do it because you count the reads), multimappers are usually not counted, though having high proportion of multimapped reads is not desired. What is the read length of your data? STAR has several options (e.g. --outFilterMismatchNmax) to restrict the n ...
written 5 weeks ago by grant.hovhannisyan1.7k
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Comment: C: Normalization of allele specific counts in RNA-seq
... Hi Ankit, To be on a safe side, you better post your question in Bioconuctor forum. The developer of DESeq2 is very responsive and helpful. ...
written 7 weeks ago by grant.hovhannisyan1.7k
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Answer: A: Normalization of allele specific counts in RNA-seq
... Michael Love (the developer of DESeq2) has written a nice manual page on how to run DESeq2 for allele-specific gene expression analysis - http://rstudio-pubs-static.s3.amazonaws.com/275642_e9d578fe1f7a404aad0553f52236c0a4.html. ...
written 7 weeks ago by grant.hovhannisyan1.7k

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Popular Question 13 days ago, created a question with more than 1,000 views. For Display pairwise p values on barplots in ggplot2
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Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Scholar 9 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
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Scholar 12 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Popular Question 3 months ago, created a question with more than 1,000 views. For Display pairwise p values on barplots in ggplot2
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Scholar 3 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
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Popular Question 6 months ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
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Scholar 6 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Popular Question 6 months ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
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Popular Question 10 months ago, created a question with more than 1,000 views. For Read counts of STAR with gff file
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Scholar 11 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
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Scholar 12 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
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