User: buchnerd

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buchnerd70
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4 years ago
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Posts by buchnerd

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Searching all proteins for a short degenerate consensus sequence
... Great, thanks! Also found a website that can do it: http://www.genome.jp/tools/motif/MOTIF2.html ...
written 4.1 years ago by buchnerd70
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Searching all proteins for a short degenerate consensus sequence
... Is there a way to search all human or mouse protein sequences for a short (~5 amino acids) degenerate amino acid sequence? ...
R sequence blast written 4.1 years ago by buchnerd70 • updated 4.1 years ago by tlawrence360
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Comment: C: Cufflinks, Warning: Skipping Large Bundle
... Nope, haven't figured it out. Increasing the bundle size didn't seem to work. ...
written 6.4 years ago by buchnerd70
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Comment: C: Cufflinks, Warning: Skipping Large Bundle
... Tried increasing to a bundle size of 100,000,000 and then 10,000,000,000. Neither one worked. ...
written 6.6 years ago by buchnerd70
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Cufflinks, Warning: Skipping Large Bundle
... I am trying to analyze mouse RNA-seq expression data but am getting the following error during cuffmerge: 8:119910359-124345724 Warning: Skipping large bundle I'm using Ensemble m38.69 (Accession #GCA_000001635.2). It seems that there is a giant gene annotated in that interval, GM20388. I ...
cufflinks cuffmerge rna-seq written 6.6 years ago by buchnerd70 • updated 6.6 years ago by Istvan Albert ♦♦ 80k
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Cufflinks Or Cuffdiff (Or Both) For Frag-Bias-Correct?
... Both Cufflinks and Cuffdiff have a frag-bias-correct option (-b). Does it matter at which step I use this option or if I use it at both steps? Same question for -u/--multi-read-correct Thanks! ...
rna-seq written 7.1 years ago by buchnerd70 • updated 7.1 years ago by Ryan Thompson3.4k
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How To Get Equal Numbers Of Gene_Id And Exon_Id For Use In Newexoncountset Function For Dexseq
... I'm trying to run DEXseq but am having trouble with the newExonCountSet function because my geneid list and exonid list are different sizes. When I unlist the mm10 geneid dataset from UCSC annotated with Ensembl Genes (ensGene) it yields 351,862 geneids even though the corresponding exonid dataset ...
rna-seq written 7.2 years ago by buchnerd70

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Popular Question 6.0 years ago, created a question with more than 1,000 views. For Cufflinks, Warning: Skipping Large Bundle
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Cufflinks Or Cuffdiff (Or Both) For Frag-Bias-Correct?

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