User: aj123
aj123 • 70
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Posts by aj123
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... 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
aj123 • 70
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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! ...
written 18 days ago by
aj123 • 70
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... 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 ...
written 2.1 years ago by
aj123 • 70
• updated
2.1 years ago by
Frédéric Bigey • 260
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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
aj123 • 70
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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?
...
written 2.1 years ago by
aj123 • 70
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... 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.
...
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Comment:
C: Paired end alignment issue
... yes thank you that answered my question. ...
written 2.1 years ago by
aj123 • 70
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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
aj123 • 70
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... 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. ...
written 2.1 years ago by
aj123 • 70
• updated
2.1 years ago by
Antonio R. Franco • 3.7k
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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
aj123 • 70
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