User: Adrian Pelin

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Adrian Pelin2.4k
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Comparative and Population Genomics of Microsporidia. Comparative and Functional Genomics of Cryptomycotans.

Posts by Adrian Pelin

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Need opinion on correct bioinfo analysis; NGS on virus competition exp
... Hi all, We took Vaccinia virus, dsDNA virus which has about 200 genes and removed roughly 30 genes from it, let call this deleted_Vaccinia. We then cloned these genes back in deleted_Vaccinia individually, so we have 30 viruses, each with a different viral gene. We pooled these together and passage ...
abundace rna-seq written 3 hours ago by Adrian Pelin2.4k
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Comment: C: How can I get in touch with a Biostars admin? Need email change.
... OK I did that. I am logging in through google and it seems that even after I changed the email, I still need to login through the old email. ...
written 6 months ago by Adrian Pelin2.4k
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Comment: A: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hello, really liking the tool so far. What base level is the log in logFC? Do you suggest log10 or log2? Thanks, A ...
written 6 months ago by Adrian Pelin2.4k
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Advice on DE analysis of mouse and human merged RNA-seq data
... Hey everyone, I wanted some advice on the way I am planning on analyzing my samples in terms of if it's done properly and if statistically sound. My biological question is: What is common between human and mouse cancer cell lines in how they deal with Vaccinia infection in terms of transcriptiona ...
mouse deseq human rna-seq written 6 months ago by Adrian Pelin2.4k • updated 5 months ago by swbarnes27.5k
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Answer: A: Ka/Ks (Or Dn/Ds) Calculation From Sequenced Transcriptome Contigs
... If you can generate a translational alignment for each of your suspected orthologous group, you can use codeml ...
written 7 months ago by Adrian Pelin2.4k
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Comment: C: Crazy high file size for human genome from Ensembl
... That makes a lot of sense! So if I just download the "primary_assembly" I would have a smaller decompressed file size only at the expense of haplotypes, is that a fair prediction? Thanks ...
written 7 months ago by Adrian Pelin2.4k
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Crazy high file size for human genome from Ensembl
... Hello, When I download release 95 repeats soft masked file "ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.toplevel.fa.gz" it is ~1 Gb, however if I decompress it, it becomes 54 Gb. This is curious as the same soft repeat masked mouse genome decompressed is ...
ensembl written 7 months ago by Adrian Pelin2.4k • updated 7 months ago by Emily_Ensembl20k
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Comment: C: How can I reproduce features of signalp TMHMM and phobius?
... I think what you are asking for is what other programs aside from the ones you mentioned can do the same thing? ...
written 7 months ago by Adrian Pelin2.4k
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Comment: C: List of human protein coding genes with given name (known function?)
... Makes a lot of sense, thanks. So I just did "`cat Homo_sapiens.GRCh38.95.gtf | grep "gene_biotype \"protein_coding\"" > Homo_sapiens.GRCh38.95.protein_coding.gtf`", is that ok in terms of creating a new gtf file? ...
written 7 months ago by Adrian Pelin2.4k
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List of human protein coding genes with given name (known function?)
... Hello, To put it simply, I am doing differential expression analysis on human RNA-seq data and I want to focus my analysis of genes that are: 1) Protein coding, so no SNOR or MIR 2) Genes with a given name (I see genes like AC006064.5 and I am not sure what they are) I am hoping that by refocusing ...
annotation rna-seq human written 7 months ago by Adrian Pelin2.4k

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Recombination detection from command line?
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Teacher 15 months ago, created an answer with at least 3 up-votes. For C: Demultiplexing fastq files. Undocumented Illumina feature.
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
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Great Question 15 months ago, created a question with more than 5,000 views. For MrBayes: Implementing the LG model

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