User: juan.crescente

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7 months ago
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Posts by juan.crescente

<prev • 76 results • page 1 of 8 • next >
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Comment: C: Understanding DESeq2 padj and Volcano Plot
... very helpful! thank you ...
written 7 months ago by juan.crescente40
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Comment: C: Understanding DESeq2 padj and Volcano Plot
... Can you point me what is the correct way to do the analysis with DESeq2? Should I use a FC cutoff prior to doing the volcano plot in DESeq2? ...
written 7 months ago by juan.crescente40
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Comment: C: Understanding DESeq2 padj and Volcano Plot
... hey thanks for answering! Should I select all values below padj<0.05 no matter the log2foldchange? Because DESeq2 is selecting all below that and it's inconsisten with the volcano plot, which seems to suggest both variables ...
written 7 months ago by juan.crescente40
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Understanding DESeq2 padj and Volcano Plot
... I'm using DESeq2 for a differential expression analysis of sRNA data. The R code looks like this: library("DESeq2") alpha <- 0.05 setwd(dirname(rstudioapi::getActiveDocumentContext()$path)); getwd() data_path <- "/home/juan/Desktop/juan/bio/mirna_mrcv/data/counts.valid.csv ...
volcano deseq2 rna-seq deg expression written 7 months ago by juan.crescente40
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Comment: C: Circular phylogenetic tree with links between leaves
... nope! I want a link, a line, between the leaves ...
written 7 months ago by juan.crescente40
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Answer: A: How to figure out which adapter has been used
... According to the authors, I ended up doing this: gunzip -c ${file_name}.fastq.gz | fastx_clipper -Q33 -l 21 | fastx_trimmer -Q33 -l 21 | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' > ${file_name}.trimmed.21.fasta so I kept the first 21bp and dismissed the rest ...
written 8 months ago by juan.crescente40
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Circular phylogenetic tree with links between leaves
... Hi! I want to create a phylogenetic tree (a circos-like plot) with links between the leaves (linked by an external relation). I've been searching for options but couldn't find any. Should be suitable for publication any ideas? ...
phylogenetic circos tree plot written 8 months ago by juan.crescente40
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Filtering tblastn results
... I have a protein sequence of a gene of interest I got from uniprot. I also have the full genomic sequences of my plant. I want to map where the gene is or if there are multiple copies. Since tblastn does not have many filtering options I started to manually filtering the best hits with high % of id ...
genome gene alignment tblastn blast written 8 months ago by juan.crescente40 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: Removing adaptors from smallRNA seq data
... I should only keep thos 61.7% of reads and then quality trim them? Is there a way to keep only those with trimmomatic? what I'm seeing is that it keeps all the reads ...
written 9 months ago by juan.crescente40
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Comment: C: Removing adaptors from smallRNA seq data
... yes! that part looks good. The problem now is that I still see a huge and only peak in 34nt. I'm expecting to see 21 and 24 peaks (and some more). ...
written 9 months ago by juan.crescente40

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Popular Question 7 months ago, created a question with more than 1,000 views. For bowtie2-build index files missing
Scholar 8 months ago, created an answer that has been accepted. For A: Odd max query limit in BLAT
Popular Question 8 months ago, created a question with more than 1,000 views. For How to count fasta sequences efficiently using (or not ) biopython
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Popular Question 13 months ago, created a question with more than 1,000 views. For How to count fasta sequences efficiently using (or not ) biopython
Scholar 18 months ago, created an answer that has been accepted. For A: Odd max query limit in BLAT
Scholar 22 months ago, created an answer that has been accepted. For A: Odd max query limit in BLAT

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