User: Biogeek

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Biogeek280
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Posts by Biogeek

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Comment: C: Genome-aligned RNA-Seq: one treatment showing high% of unmapped reads:too short
... Bets programs that can delineate contamination from .fastq? ...
written 1 day ago by Biogeek280
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Comment: C: Genome-aligned RNA-Seq: one treatment showing high% of unmapped reads:too short
... Hey Michael, I've done so. I took a proportion of those unmapped reads as fastq and converted to fasta. seems a lot are coming back as fungi and bacteria. As such, I'm gonna assemble a de novo transcriptome of all those reads and annotate the entirety of unmapped reads... OR is there an easier alte ...
written 1 day ago by Biogeek280
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Comment: C: Genome-aligned RNA-Seq: one treatment showing high% of unmapped reads:too short
... 75bp PE reads, sjdboverhang set to read length-1 ...
written 2 days ago by Biogeek280
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Comment: C: Genome-aligned RNA-Seq: one treatment showing high% of unmapped reads:too short
... I'm going back and seeing if sorting .FastQ files has any affect. ...
written 2 days ago by Biogeek280
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Genome-aligned RNA-Seq: one treatment showing high% of unmapped reads:too short
... My issue is with recent RNA-seq data we have. I've aligned my RNA-seq reads to the genome with STAR. The animal is a cnidarian at question. We have a control set of reps and a treated set of reps. Only the treated set are showing poor alignment rates. RNA extraction, enrichment and sequencing were p ...
gc content mapping rna-seq low alignment written 2 days ago by Biogeek280
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Conditional reciprocal blast confusion
... Dear all, I have 2 assemblies. A de novo assembly and a draft genome assembly of an organism. My aim is to confirm that specific genes of the de novo do in fact appear in the draft genome. I will then design primers around the best match obtained form the CRB analysis. I am using crb-blast: https: ...
crb-blast written 7 months ago by Biogeek280
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QTL /linkage trait mapping
... Hey guys, Quick and basic question: I'm on for advancing my skills in bioinformatics, having specialized in transcriptomics for a few years now. I want to delve into QTL linkage mapping in plants. Any good sources to learn from/ complete some tutorials/ practicals? Many thanks for any advice/ s ...
qtl / linkage trait mapping written 8 months ago by Biogeek280 • updated 8 months ago by andrew.j.skelton735.3k
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Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... Sorry for being ignorant. I'm unsure how I can feed the above hclustfun into my code. Can you explain how I incorporate that into heatmap.2(....)?Thanks. ...
written 11 months ago by Biogeek280
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Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... heatmap.2(lc2, col=colfunc(200),Colv= F, main = "Sample",dendrogram = "both", scale = "none", trace = "none", keysize = 1.0, key.ylab = NA, density.info = "none",key.xlab = "Z-score", labRow = "", breaks = seq(-2, 2, length.out = 201))) My code above, is there a way to do this in that? I'm just usi ...
written 11 months ago by Biogeek280
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Comment: C: Heatmap.2 - flip dendrogram so control group appears on LHS?
... I will see what I can do. Would it matter if I didn't provide the top dendrogram (Vcol = FALSE) . That command allows me to have control on LHS but just no dendrogram. ...
written 11 months ago by Biogeek280

Latest awards to Biogeek

Popular Question 7 months ago, created a question with more than 1,000 views. For EdgeR filter thresholds
Popular Question 7 months ago, created a question with more than 1,000 views. For curating a viridiplantae database
Popular Question 7 months ago, created a question with more than 1,000 views. For Low number of differentially expressed genes
Popular Question 7 months ago, created a question with more than 1,000 views. For Stand alone Blast annotation with multiple databases
Popular Question 7 months ago, created a question with more than 1,000 views. For Parsing uniprot .dat files
Popular Question 7 months ago, created a question with more than 1,000 views. For Going from BlastX to GO annotation
Popular Question 7 months ago, created a question with more than 1,000 views. For Biological variation within replicate groups, not much DE
Popular Question 7 months ago, created a question with more than 1,000 views. For Can you pool individuals to make 1 biological replicate?
Popular Question 7 months ago, created a question with more than 1,000 views. For Heatmap.2 - flip dendrogram so control group appears on LHS?
Popular Question 7 months ago, created a question with more than 1,000 views. For Time-series or pairwise comparison EdgeR - what's more suited?
Popular Question 7 months ago, created a question with more than 1,000 views. For Annoying STAR aligner problem
Popular Question 7 months ago, created a question with more than 1,000 views. For Alignment of seq reads to a genome, process after STAR?
Popular Question 7 months ago, created a question with more than 1,000 views. For normalized FPKM matrix file EdgeR and GO Mapping
Popular Question 7 months ago, created a question with more than 1,000 views. For Low number of differentially expressed genes
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Popular Question 11 months ago, created a question with more than 1,000 views. For normalized FPKM matrix file EdgeR and GO Mapping
Great Question 24 months ago, created a question with more than 5,000 views. For MDS plots with R
Epic Question 24 months ago, created a question with more than 10,000 views. For MDS plots with R
Popular Question 24 months ago, created a question with more than 1,000 views. For Can you pool individuals to make 1 biological replicate?
Popular Question 24 months ago, created a question with more than 1,000 views. For MDS plots with R
Popular Question 2.0 years ago, created a question with more than 1,000 views. For FPKM values / Data analysis
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Scholar 2.5 years ago, created an answer that has been accepted. For A: Visualize groups of conditions bys MDS.
Student 2.6 years ago, asked a question with at least 3 up-votes. For Filtering by FPKM, opinions and thoughts

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