User: aj123

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aj12370
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Posts by aj123

<prev • 66 results • page 1 of 7 • next >
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Comment: C: Expanding a case vs control analysis
... thanks for your response! I will def try exploring these avenues. This is basically case vs control samples (bam files) I have for a human disease. Just doing a DE analyses to see DE genes of interest. Hence was trying to see what other analyses/layers I could add to this. ...
written 12 days ago by aj12370
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Expanding a case vs control analysis
... Hi, Im currently doing a simple case vs control analysis on RNA Seq data. I have WGS and SNP data as well. I was wondering what are the different layers and additional analyses I could add on to my work? thanks! ...
R next-gen rna-seq snp written 18 days ago by aj12370
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RNA Seq pipeline
... Hi, Im trying to create a simple RNA Seq pipeline from fastqc to DE in python (or perl). I want to read in a configuration file with paired end data like this: Sample1 x_1.fastq x_2.fastq Sample 2 y_1.fastq y_2.fastq I would want to read it into an array and pull out each filename. P ...
perl python pipeline rna-seq sequencing written 2.1 years ago by aj12370 • updated 2.1 years ago by Frédéric Bigey260
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Comment: C: Protein interaction network
... ![enter image description here][1]This is for Mouse data. Yes, I am able to load the entire PPI data into Cytoscape. The data is in this form (attached picture). Interactor A and B are the gene names. [1]: http://s33.postimg.org/peyn8aoen/interaction_sample.jpg ...
written 2.1 years ago by aj12370
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Protein interaction network
... Hello, I have a list of genes for an organism. I want to pull out the first neighbor i.e the first protein/gene the organism is interacting with from the overall PPI network of the organism. Any suggestions on how I could do this? ...
ppi protein network cytoscape written 2.1 years ago by aj12370
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Adaptor trimming file input
... Hi all, I am using trim_galore for adaptor trimming. I would like to know if I can give several paired end data sequences like this: trim_galore w_1.fastq w_2.fastq x_1.fastq x_2.fastq z_1.fastq z_2.fastq and so on. I have included the `--paired` and other arguments. ...
adaptor rna-seq sequencing written 2.1 years ago by aj12370 • updated 2.1 years ago by geek_y8.6k
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Comment: C: Paired end alignment issue
... yes thank you that answered my question. ...
written 2.1 years ago by aj12370
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Comment: C: Paired end alignment issue
... Does it matter if the unmapped sequences files are larger than the accepted hits.bam file? ...
written 2.1 years ago by aj12370
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Paired end alignment issue
... Hi, I have paired end data which im trying to align using tophat: tophat -r 200 -p 4 -o /.../Tophat_output/ -G /pathtogtf /pathtobowtieindexfiles Sample10_untrim1.fastq Sample10_untrim2.fastq Im getting only one bam alignment file. Im not sure if I should be getting 2 bam files. ...
paired end tophat alignment bowtie sequencing written 2.1 years ago by aj12370 • updated 2.1 years ago by Antonio R. Franco3.7k
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Comment: C: Gene Ontology mining from IDs
... Hi Denise-interested in Human and Mouse. thank you. ...
written 2.1 years ago by aj12370

Latest awards to aj123

Popular Question 18 days ago, created a question with more than 1,000 views. For RNA Seq pipeline
Popular Question 20 months ago, created a question with more than 1,000 views. For RNA Seq pipeline
Popular Question 20 months ago, created a question with more than 1,000 views. For Gene Ontology mining from IDs
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