User: Adrian Pelin

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Adrian Pelin2.2k
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Comparative and Population Genomics of Microsporidia. Comparative and Functional Genomics of Cryptomycotans.

Posts by Adrian Pelin

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Comparing NCI-60 transcriptome with another variable to determine genes that correlate
... Hello, I will probably not formulate this properly but I want to compare the transcriptome of NCI-60 cell lines with the ability of my virus to kill these cell lines. Ideally, I want to find genes whose expression correlates with ability of virus to kill that cell. There used to be a tool called CO ...
rna-seq nci60 written 4 weeks ago by Adrian Pelin2.2k • updated 4 weeks ago by cannin250
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Comment: C: bash & quickGO to download gene symbols of a GO term
... This is pretty sweet! Thanks! ...
written 4 weeks ago by Adrian Pelin2.2k
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Comment: C: bash & quickGO to download gene symbols of a GO term
... Yeah I noticed that. The problem is that it's not supposed to open as a webpage but rather as a tab delimited file and it's supposed to give me only taxid 9606 and not other organisms... It would defeat the point of doing this in bash if I were to manually download entries every time, was hoping to ...
written 8 weeks ago by Adrian Pelin2.2k
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bash & quickGO to download gene symbols of a GO term
... Hello, there is a very old post (https://www.biostars.org/p/52101/) that shows you can download data from quickGO using bash by using something like this: curl -s "http://www.ebi.ac.uk/QuickGO/GAnnotation?tax=9606&relType=IP&goid=%20GO:0009615%20&format=tsv" For some reason there i ...
annotations go bash written 8 weeks ago by Adrian Pelin2.2k • updated 5 weeks ago by EagleEye6.1k
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Comment: C: RNA-seq analysis of virally infected cells
... I do not mean to advertise products here, but when you say spike-in normalization, do you mean something like this: https://www.thermofisher.com/order/catalog/product/4456739 ? Are there better, maybe cheaper options out there? ...
written 4 months ago by Adrian Pelin2.2k
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Comment: C: RNA-seq analysis of virally infected cells
... What do you mean by global change? You mean that overall there is more viral genes in one condition compared to another, for instance more viral reads? ...
written 4 months ago by Adrian Pelin2.2k
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Comment: C: RNA-seq analysis of virally infected cells
... Duplicates, and multiple time points, but 12h is a more crucial one for us. ...
written 4 months ago by Adrian Pelin2.2k
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Answer: A: FPKM matrix after stringtie using ballgown
... Not sure you need ballgown to get FPKMs. My understanding is ballgown is needed for differential analysis, stringtie can output TPM and FPKM. When I run stringite, I pass the argument "-A output_dir/gene_abundances.tsv", and the gene_abundances.tsv has FPKM and TPM. Hope this helps, A ...
written 4 months ago by Adrian Pelin2.2k
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RNA-seq analysis of virally infected cells
... I have a human cancer cell line infected with 2 different vaccinia pox viruses (~200 kb dsDNA genome, 200 genes). At 12 hours post infection I harvested my RNA and send for RNA-seq. It looks like for strain_A, 40% reads are viral (60% host) while strain_B 60% reads are viral (40% host). This makes ...
host rna-seq virus written 4 months ago by Adrian Pelin2.2k • updated 10 weeks ago by Biostar ♦♦ 20
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Comment: C: Anybody Managed To Make Inparanoid Work?
... I find orthoMCL to do the job better, that's why I gave up on inparanoid. ...
written 14 months ago by Adrian Pelin2.2k

Latest awards to Adrian Pelin

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Loss of Heterozygosity from VCF file in non-model organisms
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Recombination detection from command line?
Great Question 4 weeks ago, created a question with more than 5,000 views. For MrBayes: Implementing the LG model
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Demultiplexing fastq files. Undocumented Illumina feature.
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 4 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 4 months ago, created a question with more than 1,000 views. For Loss of Heterozygosity from VCF file in non-model organisms
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Demultiplexing fastq files. Undocumented Illumina feature.
Popular Question 4 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Great Question 13 months ago, created a question with more than 5,000 views. For bwa mem vs bwa aln
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Nextera Transposon Contamination
Popular Question 13 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 13 months ago, created a question with more than 1,000 views. For Loss of Heterozygosity from VCF file in non-model organisms
Popular Question 13 months ago, created a question with more than 1,000 views. For bwa report multiple alignments
Great Question 13 months ago, created a question with more than 5,000 views. For Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question 13 months ago, created a question with more than 1,000 views. For Strategy to get rid of fake mate pairs
Popular Question 13 months ago, created a question with more than 1,000 views. For DiscoSnp++, question about how SNPs called
Popular Question 13 months ago, created a question with more than 1,000 views. For UCSC_TFBS enrichment with DAVID
Popular Question 13 months ago, created a question with more than 1,000 views. For RNA-seq experiment of mouse organs
Popular Question 13 months ago, created a question with more than 1,000 views. For VCFTools: Calculation of r^2 fails
Popular Question 13 months ago, created a question with more than 1,000 views. For Predict AA sequence from assembled transcripts
Popular Question 13 months ago, created a question with more than 1,000 views. For Extracting paired-end reads on different contigs from bam file
Popular Question 13 months ago, created a question with more than 1,000 views. For Plotting sequence similarity/identity of a multiple sequence alignment
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Average coverage of de novo SPAdes assembly deviates a lot from theretical cover
Popular Question 13 months ago, created a question with more than 1,000 views. For Calling large indels from NGS

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