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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Comment: C: How to get percent identity from bam file ?
... Sorry Pierre but I think the original question asked a read by read assessment of percent identity, rather than histogram. I was looking for that as well. Is there any way to tailor this so that one column is read name and second column is percent identity to ref? Thanks ...
written 4 weeks ago by Adrian Pelin2.2k
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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 3 months ago by Adrian Pelin2.2k • updated 3 months 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 3 months 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 4 months 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 4 months ago by Adrian Pelin2.2k • updated 3 months ago by EagleEye6.2k
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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 6 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 6 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 6 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 6 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 6 months ago by Adrian Pelin2.2k • updated 4 months ago by Biostar ♦♦ 20

Latest awards to Adrian Pelin

Student 5 weeks ago, asked a question with at least 3 up-votes. For MrBayes: Implementing the LG model
Great Question 3 months ago, created a question with more than 5,000 views. For MrBayes: Implementing the LG model
Popular Question 3 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 3 months ago, created a question with more than 1,000 views. For Loss of Heterozygosity from VCF file in non-model organisms
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: Demultiplexing fastq files. Undocumented Illumina feature.
Popular Question 3 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 6 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: Demultiplexing fastq files. Undocumented Illumina feature.
Popular Question 6 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 6 months ago, created a question with more than 1,000 views. For Loss of Heterozygosity from VCF file in non-model organisms
Great Question 15 months ago, created a question with more than 5,000 views. For bwa mem vs bwa aln
Popular Question 15 months ago, created a question with more than 1,000 views. For MrBayes chains converged, how to stop early?
Great Question 15 months ago, created a question with more than 5,000 views. For MrBayes: Implementing the LG model
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Nextera Transposon Contamination
Great Question 15 months ago, created a question with more than 5,000 views. For Unexpected outcome: Gene Enrichment using Fisher's Test
Popular Question 15 months ago, created a question with more than 1,000 views. For Calling large indels from NGS
Popular Question 15 months ago, created a question with more than 1,000 views. For Strategy to get rid of fake mate pairs
Popular Question 15 months ago, created a question with more than 1,000 views. For UCSC_TFBS enrichment with DAVID
Popular Question 15 months ago, created a question with more than 1,000 views. For RNA-seq experiment of mouse organs
Popular Question 15 months ago, created a question with more than 1,000 views. For bwa report multiple alignments
Popular Question 15 months ago, created a question with more than 1,000 views. For Loss of Heterozygosity from VCF file in non-model organisms
Popular Question 15 months ago, created a question with more than 1,000 views. For Plotting sequence similarity/identity of a multiple sequence alignment
Popular Question 15 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 15 months ago, created a question with more than 1,000 views. For Comparing RNAseq Samples

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