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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... Also, to your other question, how did I handle the 170 genes. I didn't do anything special... I am not sure how much should I care about them. I care about how abundance (fold change) of each one of the 30 genes changes between input and output. The 170 genes are present in 100% of viruses, so they ...
written 6 months ago by
Adrian Pelin • 2.4k
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... Amazing question!
seal.sh:
${bbmap}/seal.sh -Xmx40g threads=16 ref=Copenhagen_M35027_CDS_v2.fasta in=reads/${i}_AdaptTrim_R#.fastq.gz stats=seal_stats/${i}
In the fasta file... each fasta contig ">" is a gene from ATG to stop. So there are 200 contigs in the fasta file for each gene. ...
written 6 months ago by
Adrian Pelin • 2.4k
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... Those 30 viruses were pooled. The only difference between them is which of the 30 genes they encode. Overall, 170 genes are the same between the 30 viruses, and each virus has one gene as a "tag" that it expresses and may make it a better replicating virus or worse. So the gene coding sequence in re ...
written 6 months ago by
Adrian Pelin • 2.4k
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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 6 months 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 13 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 13 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 13 months ago by
Adrian Pelin • 2.4k
• updated
12 months ago by
swbarnes2 ♦ 8.9k
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... If you can generate a translational alignment for each of your suspected orthologous group, you can use codeml ...
written 13 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 13 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 13 months ago by
Adrian Pelin • 2.4k
• updated
13 months ago by
Emily_Ensembl ♦ 21k
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