User: aka001

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aka001190
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Posts by aka001

<prev • 37 results • page 1 of 4 • next >
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Answer: A: unique list based on multiple column
... Based on the example in one of your comments, you can do it with this: awk -F',' '!seen[$2,$4]++' your_file.txt You might have problems later on when there are multiple lines with the same 2nd and 4th columns but different values in some other columns. However, as you didn't mention it, above ...
written 2.7 years ago by aka001190
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Comment: C: classification of small RNA-seq
... Currently you are at which step (another way to put it: how did you process your reads)? ...
written 2.8 years ago by aka001190
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Comment: C: Confirming predicted gene model by RNA-Seq data
... What kind of information (of the predicted models) that you have currently: genomic coordinates, protein sequence, or? Honestly I don't really get your point on what to confirm by RNA-seq, protein or gene model? It's a bit of a more complex task (it's another story), since protein levels are not nec ...
written 2.8 years ago by aka001190
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Answer: A: classification of small RNA-seq
... Although your question seems lacking some depth and clarity, I would just point out one way (there are many ways, e.g. prediction, etc.): take the gene biotype information of your's organism Ensembl gtf file (i.e. count your reads using this file). There you can see different biotypes, including wha ...
written 2.8 years ago by aka001190
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Answer: A: RNA-Seq analysis using STAR and Salmon
... As you are mentioning Salmon, I would guess you want to count at the transcript level. You should run it for individual BAM files (without merging). As long as you have the reference (that is, annotation file of the transcriptome, not the genome file itself), Salmon should be usable. If you want to ...
written 2.8 years ago by aka001190
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Answer: A: Downloading gtf file for RefSeq
... You can get the refGene annotation file from the UCSC: [http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/][1] Just change the genome version with what you wanted. [1]: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/ ...
written 2.8 years ago by aka001190
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Comment: C: Examine a specific gene in WGCNA
... Wouldn't extract the modules is the first step to do? ...
written 2.8 years ago by aka001190
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Answer: A: Download list of all genes of genome build GRCh38.p0
... You can use Ensembl BioMart to do that. ...
written 2.9 years ago by aka001190
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Comment: C: Cuffnorm: which output file should I use
... Well, if we go back again to what you wanted in the first place, which is normalisation, it would depend of what kind of normalisation did you want. By definition, fpkm is already normalised value, but it's normalised by library size (i.e. within sample). For the next step, probably you would want t ...
written 2.9 years ago by aka001190
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Comment: C: Cuffnorm: which output file should I use
... The normalised expression should be genes.fpkm_tracking. ...
written 2.9 years ago by aka001190

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