User: Adrian Pelin
Adrian Pelin • 2.4k
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Comparative and Population Genomics of Microsporidia. Comparative and Functional Genomics of Cryptomycotans.
Posts by Adrian Pelin
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... 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 ...
written 3 hours ago by
Adrian Pelin • 2.4k
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... 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 Pelin • 2.4k
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... 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 Pelin • 2.4k
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... 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 ...
written 6 months ago by
Adrian Pelin • 2.4k
• updated
5 months ago by
swbarnes2 ♦ 7.5k
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... If you can generate a translational alignment for each of your suspected orthologous group, you can use codeml ...
written 7 months ago by
Adrian Pelin • 2.4k
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... 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 Pelin • 2.4k
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... 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 ...
written 7 months ago by
Adrian Pelin • 2.4k
• updated
7 months ago by
Emily_Ensembl ♦ 20k
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... 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 Pelin • 2.4k
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... 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 Pelin • 2.4k
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... 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 ...
written 7 months ago by
Adrian Pelin • 2.4k
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