User: syrttgump

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syrttgump30
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30
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New User
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USA/Newark/New Jersey Institute of Technology
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1 year, 3 months ago
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3 years, 3 months ago
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Posts by syrttgump

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Errors when install samtools 0.1.18 from source code
... I want to install the Perl package Bio::DB::Sam, it need this old version of samtools ...
written 19 months ago by syrttgump30
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Errors when install samtools 0.1.18 from source code
... Hi, I downloaded source code of samtools-0.1.18, then compile it by the command line: make CFLAGS=-fPIC But this is the error: gcc -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o err ...
software error samtools written 19 months ago by syrttgump30 • updated 19 months ago by Michael Dondrup45k
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Answer: A: What is an optimal normalization approach for comparing GTEx RNASeq normal vs TC
... I found this: [https://github.com/mskcc/RNAseqDB][1] Which is a datasets of normalized TCGA and GTEx RNA-Seq data. [1]: https://github.com/mskcc/RNAseqDB ...
written 20 months ago by syrttgump30
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Comment: C: WGCNA TOM file
... I found it. I can use as.matrix function. TOM data is a dist object. ...
written 23 months ago by syrttgump30
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WGCNA TOM file
... Hi All, I am using WGCNA build a coexpression network. Here is the thing: I use `blockwiseModules` to build network, and saved TOM to a file. Then I want to calculate connectivity of genes by using the TOM data. I load TOM file into R workspace, it is a large dist class object. How can I transfer it ...
wgcna written 23 months ago by syrttgump30
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Comment: C: small RNA-seq reads grouping by adjacency
... samtools ([http://www.htslib.org/doc/samtools.html][1]), you need to first sort SAM file then use samtools view to cut out certain regions. [1]: http://www.htslib.org/doc/samtools.html ...
written 23 months ago by syrttgump30
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How to let WGCNA use multiple cores
... Hi guys, I am using WGCNA to deal with some large datasets (~20000 genes on ~1000 samples). I read in the help documents that WGCNA support multi-thread to speed up calculation. But when I run functions like `blockwiseModules, TOMsimilarityFromExpr, cor` etc, I can set parameter `nThreads`, it works ...
wgcna parallel multe-thread written 23 months ago by syrttgump30 • updated 7 months ago by yplee6140
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Comment: C: Does CDS, start_codon and stop_codon in gtf affect transcriptome assembly by Str
... Thank you! I have seen the problem: now if I do differential expression analysis, I would get multiple expression values like FPKM values for only one gene, and this will make the DE result very misleading. For the GTF files, your suggest is that gencode comprehensive set had already cover all known ...
written 2.8 years ago by syrttgump30
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Comment: C: Does CDS, start_codon and stop_codon in gtf affect transcriptome assembly by Str
... Is this a problem? Is that possible that any different transcript belong to different gene? ...
written 2.8 years ago by syrttgump30
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Comment: C: Does CDS, start_codon and stop_codon in gtf affect transcriptome assembly by Str
... Thanks for comment. This is very important to me. Could you tell me where can I get the refSeq, UCSC GTF file in this format? Since I need all of refSeq, UCSC and gencode. ...
written 2.8 years ago by syrttgump30

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Popular Question 19 months ago, created a question with more than 1,000 views. For Error when install ggbio

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