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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Comment: C: Need opinion on correct bioinfo analysis; NGS on virus competition exp
... 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 9 months ago by Adrian Pelin2.4k
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Comment: C: Need opinion on correct bioinfo analysis; NGS on virus competition exp
... 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 9 months ago by Adrian Pelin2.4k
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Comment: C: Need opinion on correct bioinfo analysis; NGS on virus competition exp
... 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 9 months ago by Adrian Pelin2.4k
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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 9 months 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 16 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 16 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 16 months ago by Adrian Pelin2.4k • updated 14 months ago by swbarnes29.3k
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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 16 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 16 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 16 months ago by Adrian Pelin2.4k • updated 16 months ago by Emily_Ensembl21k

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Popular Question 11 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Demultiplexing fastq files. Undocumented Illumina feature.
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Nextera Transposon Contamination
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Biostars 3.0 is now under testing. It has groups, charms and other interesting f
Great Question 14 months ago, created a question with more than 5,000 views. For Getting Cegma/Genewise To Work On Centos, Rhel
Great Question 14 months ago, created a question with more than 5,000 views. For Any software to view newick/nexus trees command line?
Popular Question 14 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Great Question 14 months ago, created a question with more than 5,000 views. For Removing PCR duplicates from .fastq without .bam alignment
Great Question 15 months ago, created a question with more than 5,000 views. For MrBayes: Implementing the LG model
Popular Question 16 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 19 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
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Popular Question 20 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 21 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 23 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Great Question 23 months ago, created a question with more than 5,000 views. For MrBayes: Implementing the LG model
Popular Question 23 months ago, created a question with more than 1,000 views. For Loss of Heterozygosity from VCF file in non-model organisms
Student 23 months ago, asked a question with at least 3 up-votes. For MrBayes: Implementing the LG model
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For C: Demultiplexing fastq files. Undocumented Illumina feature.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Loss of Heterozygosity from VCF file in non-model organisms
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Recombination detection from command line?
Great Question 2.1 years ago, created a question with more than 5,000 views. For MrBayes: Implementing the LG model

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