User: grant.hovhannisyan

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Posts by grant.hovhannisyan

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Comment: C: Negative values HTSeq2
... do not transform you data for DESeq2, it expects raw count data ...
written 4 months ago by grant.hovhannisyan2.0k
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Answer: A: RNA seq data analysis
... I recently recorded a video for students covering the very basic steps for dif. expression analysis using RNA-Seq, though it does not cover data fetching from databases. Hope it helps to grasp the basics https://www.loom.com/share/a55c1dedb8e64e7cac47f6595b751de7 ...
written 6 months ago by grant.hovhannisyan2.0k
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Comment: C: Error while running CPAT
... good. then you can accept my answer to close the thread ...
written 6 months ago by grant.hovhannisyan2.0k
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Comment: C: Error while running CPAT
... it seems you did´t use conda. first install miniconda (it is a package manager) https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html when installed, create a new environment, for example: `conda create -n env_cpat` activate the environment: `conda activate env_cpat` then ...
written 6 months ago by grant.hovhannisyan2.0k
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Comment: C: Error while running CPAT
... have you tried installing in a new environment? ...
written 6 months ago by grant.hovhannisyan2.0k
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Comment: C: Error while running CPAT
... don't know how to solve this exact dependency, but you can try installing cpat using conda, it should solve all dependencies https://anaconda.org/bioconda/cpat ...
written 6 months ago by grant.hovhannisyan2.0k
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Comment: C: Trimmomatic paired-end mode question
... which exact command have you tried running? did it throw any error? what you propose seems correct, instead of `${SRR}_1.fastq.gz`, you just need to locate you own file. You also have to specify the reverse reads, and 4 output files (forward paired, forward unpaired, reverse paired, reverse unpaired ...
written 6 months ago by grant.hovhannisyan2.0k
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Comment: C: VCF to Fasta with out reference
... how would you know what is in between the variants if you don't use reference sequence? ...
written 7 months ago by grant.hovhannisyan2.0k
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Comment: A: How do I match two files using one column as reference?
... Check `merge` function in R. ...
written 7 months ago by grant.hovhannisyan2.0k
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Comment: C: Need help with STAR aligner
... what organism do you work with? for human size genome you would need 32GB of RAM, for organisms with smaller genomes (like yeasts with 10-12 Mb), STAR alignment is doable with a modest laptop. ...
written 7 months ago by grant.hovhannisyan2.0k

Latest awards to grant.hovhannisyan

Popular Question 4 weeks ago, created a question with more than 1,000 views. For RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
Popular Question 10 weeks ago, created a question with more than 1,000 views. For RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
Great Question 10 weeks ago, created a question with more than 5,000 views. For Technical replicates in RNAseq
Popular Question 11 weeks ago, created a question with more than 1,000 views. For RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
Popular Question 5 months ago, created a question with more than 1,000 views. For Compare sets of GO enrichments
Popular Question 6 months ago, created a question with more than 1,000 views. For Compare sets of GO enrichments
Popular Question 6 months ago, created a question with more than 1,000 views. For Compare sets of GO enrichments
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Popular Question 9 months ago, created a question with more than 1,000 views. For STAR for bacterial genome
Student 9 months ago, asked a question with at least 3 up-votes. For Technical replicates in RNAseq
Popular Question 9 months ago, created a question with more than 1,000 views. For STAR for bacterial genome
Popular Question 11 months ago, created a question with more than 1,000 views. For STAR for bacterial genome
Popular Question 11 months ago, created a question with more than 1,000 views. For STAR for bacterial genome
Great Question 11 months ago, created a question with more than 5,000 views. For Read counts of STAR with gff file
Popular Question 12 months ago, created a question with more than 1,000 views. For STAR for bacterial genome
Popular Question 12 months ago, created a question with more than 1,000 views. For STAR for bacterial genome
Popular Question 16 months ago, created a question with more than 1,000 views. For Display pairwise p values on barplots in ggplot2
Popular Question 16 months ago, created a question with more than 1,000 views. For Display pairwise p values on barplots in ggplot2
Teacher 17 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Teacher 17 months ago, created an answer with at least 3 up-votes. For C: weird STAR output, bash scripting problem
Scholar 17 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Voter 18 months ago, voted more than 100 times.
Scholar 18 months ago, created an answer that has been accepted. For A: Change sequence in SEQIO
Popular Question 18 months ago, created a question with more than 1,000 views. For Display pairwise p values on barplots in ggplot2
Popular Question 19 months ago, created a question with more than 1,000 views. For Display pairwise p values on barplots in ggplot2

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