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: 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 11 weeks 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 11 weeks 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 11 weeks 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 11 weeks 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 11 weeks ago by Adrian Pelin2.2k • updated 3 days ago by Biostar ♦♦ 20
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Comment: C: Anybody Managed To Make Inparanoid Work?
... I find orthoMCL to do the job better, that's why I gave up on inparanoid. ...
written 12 months ago by Adrian Pelin2.2k
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Comment: C: Detecting junctions from reads spanning large indels
... oh I see. Both still do the same thing though, correct? ...
written 12 months ago by Adrian Pelin2.2k
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Comment: C: Detecting junctions from reads spanning large indels
... sweet, goes directly to coordinates. Is there any way to get an intermediary sam file to see which reads were counted for generating coordinates? ...
written 12 months ago by Adrian Pelin2.2k
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Detecting junctions from reads spanning large indels
... Hello, I am mapping my reads with an aligner that allows for large indels (bbmap, other suggestions welcome). I am than using SamJs to get reads that have large indels >1kb java -jar ${HOME}/programs/jvarkit/dist/samjs.jar --file get_indel_sam_filter.javascript --samoutputformat SAM -o Fas ...
dna-seq sam written 12 months ago by Adrian Pelin2.2k • updated 12 months ago by Pierre Lindenbaum114k
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Comment: C: Filter sam file to remove reads with large deletions
... Neat tool Pierre, I want to do the opposite, I want to find reads in sam file that span large deletions (>1kb), so I thought I would use your -X option, to save discarded. Running into a few issues, samoutputformat is not considered valid and -X doesn't get recognized? https://pastebin.com/k2dVRx ...
written 12 months ago by Adrian Pelin2.2k

Latest awards to Adrian Pelin

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Recombination detection from command line?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Recombination detection from command line?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For C: Demultiplexing fastq files. Undocumented Illumina feature.
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Loss of Heterozygosity from VCF file in non-model organisms
Popular Question 10 months ago, created a question with more than 1,000 views. For Recombination detection from command line?
Great Question 10 months ago, created a question with more than 5,000 views. For bwa mem vs bwa aln
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Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Nextera Transposon Contamination
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Great Question 10 months ago, created a question with more than 5,000 views. For MrBayes: Implementing the LG model

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