User: grant.hovhannisyan

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Posts by grant.hovhannisyan

<prev • 214 results • page 1 of 22 • next >
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Answer: A: Difference in FPKM values of lncRNA when using different annotation files
... IMHO, when you use only lncRNA annotations, your library size (total number of mapped reads overlapping features) is always less than when you use a comprehensive annotation. Thus, you always get higher FPKM values when you use only lncRNA annotations. There is a recent bioarxiv paper addressing thi ...
written 8 hours ago by grant.hovhannisyan970
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Comment: C: Very low unique mapped reads - STAR alignment
... have you done QC of fastq files? And are you sure that you are mapping to a correct reference genome? ...
written 1 day ago by grant.hovhannisyan970
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Comment: C: Difference between differential transcript expression and differential splicing
... To me, in differential splicing analysis you are always interested in studying different isoforms, while in case of differential transcript expression you also can be interested in assessing expression levels of the same transcript across different conditions. ...
written 4 days ago by grant.hovhannisyan970
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Comment: C: Conflict of abundances on different taxonomic levels using centrifuge
... Thanks for clarifying! This is actually exactly how I was interpreting the assignments until I have seen a Kraken file format, where everything is summarize in hierarchical manner, and that's why I thought that most probably it should be the case here as well. *you would sum the counts at the genus ...
written 9 days ago by grant.hovhannisyan970
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Conflict of abundances on different taxonomic levels using centrifuge
... I have posted this in Centrifuge github, but it doesn't to be seem very responsive. I want to analyze microbial abundances on genus level using `centrifuge`. However I see that genus level abundances (and read counts) are less than abundances of species in the corresponding genus, which seems a bit ...
centrifuge metagenomics written 9 days ago by grant.hovhannisyan970 • updated 9 days ago by Rob2.5k
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Comment: C: Sorting of SNPs which has less than 0.05 threshold P-Value
... please post some example lines from that files. ...
written 11 days ago by grant.hovhannisyan970
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Comment: C: Multiple testing correction in linear mixed models (MLM) for GWAS
... Just out of curiosity, does the statistical method (MLM in this case) matter on which type of correction to use? ...
written 12 days ago by grant.hovhannisyan970
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Comment: C: Best cutoff for fold change of microarray data
... Fold change can not be negative, but log-transformed fold change can. Imagine your initial expression is 100 and after a treatment it decreased to 50. The fold change is 0.5, and log(2) fold change is -1. ...
written 12 days ago by grant.hovhannisyan970
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Answer: A: RNA-seq illumina paired-end data simulation with fold change differences
... Not a direct answer to your question, but here you have a nice and detailed review about NGS simulation tools https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224698/. You can find there the ones that fit your goal. ...
written 13 days ago by grant.hovhannisyan970
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Comment: C: HISAT2, Stringtie,DEseq2 differential gene expression
... You can accept @Devon's answer so everyone knows that your issue is solved ...
written 13 days ago by grant.hovhannisyan970

Latest awards to grant.hovhannisyan

Student 18 days ago, asked a question with at least 3 up-votes. For Technical replicates in RNAseq
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Technical replicates in RNAseq
Scholar 10 weeks ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Read counts of STAR with gff file
Scholar 4 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: gatk tool installation problem
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Scholar 5 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Scholar 5 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Centurion 5 months ago, created 100 posts.
Scholar 5 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Supporter 11 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Teacher 11 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
Scholar 13 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO

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