User: DataFanatic

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DataFanatic150
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Posts by DataFanatic

<prev • 79 results • page 1 of 8 • next >
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Extracting related sequences from a FASTA file
... How can I 1. Compare long genomic sequences e.g 1-15kb and group them into families 2. Look for a specific k-mer within these sequences 3. FInd most frequently shared k-mers Thank you! ...
sequence comparizon data mining kmer written 15 months ago by DataFanatic150 • updated 13 months ago by Biostar ♦♦ 20
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Bulk primer design
... Given a FASTA sequence, how can I design primers specifying the desired number of primers and a distance? e.g Generate 100 primers every 500bp. Thank you! ...
fasta bulk primers kmer written 15 months ago by DataFanatic150 • updated 15 months ago by Pierre Lindenbaum126k
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Comment: C: where to keep scripts for new software
... Yes,I apologize if this is not within the bioinformatics subject, but it is certainly a fundamental (basic but fundamental) concept also used in bioinformatics. How can one create a symlink from $HOME/path/to/package to $HOME/bin Thank you!! ...
written 16 months ago by DataFanatic150
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where to keep scripts for new software
... When downloading software in a unix system to a bin directory $HOME/bin a new directory containing the scripts is created $HOME/bin/packagedir adding this to the path everytime you download a new package makes the $PATH long and complicated. Would you advice to transfer all the scripts from the or ...
$path install unix written 16 months ago by DataFanatic150
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Comment: C: Pacbio inversion visualization and IGV
... Picasa , Did you figure this out? ...
written 17 months ago by DataFanatic150
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Comment: C: GMAP download page
... Thank you for your answer, Yes I am referring to GMAP. Let me clarify my second question: I only have a PC/Mac **and** **no** Unix server. Can I install SMRTLink on my Mac/PC?? Also, is GMAP a good alternative to SMRTLink? I need to detect gene isoforms without a reference. ...
written 17 months ago by DataFanatic150
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GMAP download page
... I am interested in analyzing PacBio long read (full transcript) RNAseq data using GMAP; however, GMAP download page seems to have been removed. Does anyone know if GMAP is still available for download? PacBio have their own software SMRTlink software but I believe this will not run on windows or mac ...
gmap rna-seq pacbio written 17 months ago by DataFanatic150
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Answer: A: differential gene expression analysis
... Devon, How can I plot the data going into the analysis? design<-model.matrix(~group+batch+RIN) will include RIN in the model and this should change the way samples cluster by PCA or MDS plot. Is there a way to extract the corrected counts matrix? Thank you! ...
written 21 months ago by DataFanatic150
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Comment: A: differential gene expression analysis
... Is there a way to visualize the data (residuals) using PCA or MDS plot after performing the linear modeling? I want to do this to confirm the samples no longer cluster by batch. ...
written 21 months ago by DataFanatic150
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Comment: A: differential gene expression analysis
... "Yes, typically one simply adds batch and RIN as covariates if they seem relevant. " Do you mean that you can add covariates into the model matrix e.g. design<-model.matrix(~group+batch+RIN) Thanks! ...
written 21 months ago by DataFanatic150

Latest awards to DataFanatic

Great Question 15 months ago, created a question with more than 5,000 views. For merging two bigwig files
Popular Question 15 months ago, created a question with more than 1,000 views. For Filter out related individuals from a vcf file using Plink or Hail
Popular Question 15 months ago, created a question with more than 1,000 views. For merging two bigwig files
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Supporter 2.4 years ago, voted at least 25 times.
Popular Question 2.8 years ago, created a question with more than 1,000 views. For merging two bigwig files

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