User: kennethcondon2007

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Posts by kennethcondon2007

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Comment: C: ensembl transcript id to gene symbol using biomart
... take a look at the id history on the website ...
written 4 days ago by kennethcondon2007810
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Comment: C: Experiences with large datasets
... That said you should always (where possible) get the fastq files directly from EBI-ENA and avoid sratoolkit/sra files. - why? ...
written 6 weeks ago by kennethcondon2007810
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Comment: C: Experiences with large datasets
... Are you able to provide details on the capacity of your University cluster (No. of cores, RAM per core etc)? Also, have you ever completed a run for a single SRA file...just to get a feel for expected time to run? On any of the runs can you get a print out of the max memory usage? Are you able to re ...
written 6 weeks ago by kennethcondon2007810
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Comment: C: Weird translated refs between hg19 and hg38
... Cant' provide an answer but the posts below may be of use. Cross species mapping is something I'm beginning to look into. Crosmap is the basis for the Ensembl API. So maybe try the Ensembl API to see if it returns the same issue? https://www.biostars.org/p/65558/ https://www.biostars.org/p/70648/ ...
written 7 weeks ago by kennethcondon2007810
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Answer: A: How to rank genes prepared for GSEA analysis with TopGO
... You are correct in "the significance of the difference is reflected by two metrics" but they are p-value and FDR (or p-value and q-value depending on the program you use). Fold change is actually the difference between the expression values between the 2 groups. If you used deseq then fold = concS ...
written 7 weeks ago by kennethcondon2007810
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Comment: C: Define exact peak borders
... To clarify: you want the red bar to be the same length as the blue bar or as the blue peak region? What about peak center +/- total fragment length? More importantly....what is the purpose of defining the borders? what are you trying to achieve by doing this? ...
written 7 weeks ago by kennethcondon2007810
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Comment: C: RNA Seq data network analysis
... Co- expression analysis is not the only way to create a network. You only need to find a set of genes with something in common...for example a list of differentially expressed genes. Use [DESEQ2][1] to calculate differential expression between samples....then get the list of genes that are differen ...
written 8 weeks ago by kennethcondon2007810
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Comment: C: cutadapt error while performing Trim_Galore
... I think line 1 is just the file it is currently reading.... it clearly processes the first 40 million sequences. Sounds like you'll have to do some file extraction work in the shell to find the line causing the error. I would make a test file of the first 40 million sequences to see if it completes. ...
written 8 weeks ago by kennethcondon2007810
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Comment: A: RNA Seq data network analysis
... Could you be more specfic about what you mean by "network analysis"? ...
written 8 weeks ago by kennethcondon2007810
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Comment: C: Displaying genes in genome browsers
... You must remember that the database you get the sequence from only stores the sequence of the gene as if it was transcribed in the forward direction. For example: If a gene is transcribed in the reverse direction (GGGAAACCCTTT) the database will still only store AAAGGGTTTCCC as if it is transcribed ...
written 8 weeks ago by kennethcondon2007810

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For RNA-seq RPKM significance cut off
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