User: Russ

gravatar for Russ
Russ160
Reputation:
160
Status:
Trusted
Location:
Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
Last seen:
2 days, 17 hours ago
Joined:
2 years, 5 months ago
Email:
r*******@uoguelph.ca

Posts by Russ

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Get counts from Balgown for differential expression by suing DeSeq2
... No, you shouldn't combine replicates. They should each be aligned independently and then the correlation between your replicates checked in subsequent analysis. The data from each replicate should be present - and annotated as such - when input into DESeq2. To get the counts for DESeq2, you need to ...
written 6 days ago by Russ160
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Answer: A: Number of SNPs in VCF
... So if I understand correctly, you have a VCF file with about 1000 samples that represent 7 different breeds of animal. Each sample is named in a consistent fashion, with a prefix (e.g. "FLV" or "SIM") and then a number. You could use GATKs [SelectVariant][1] tool to subset your VCF into 7 files, on ...
written 11 days ago by Russ160
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Answer: A: Identifying miRNA, RNA-binding sites in UTRs
... For non-model organisms information can be sparse. [miRBase][1] has miRNA sequences from a wide variety of species. You can try combining the sequences obtained from miRBase with TargetScan and miRanda to help predict miRNA binding sites in non-model organisms. [1]: http://www.mirbase.org/ ...
written 20 days ago by Russ160
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Comment: C: Selecting fastq sequences
... I think it's worth highlighting that you can re-loop through a file by using `seek()` to start iterating back at the beginning of the file (as noted in the link you posted). Also, strongly agree about commenting. I've come back to a number of my quick, un-commented scripts only to spend time trying ...
written 4 weeks ago by Russ160
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Comment: C: Unusual reports from "bcftools stats" (making me question my data)
... No need to apologize! You provided a nice succinct answer, my additions would be redundant :) Cheers. ...
written 4 weeks ago by Russ160
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Comment: C: Unusual reports from "bcftools stats" (making me question my data)
... I had typed out an answer but Kevin beat me (and did a better job). I think it's probably still worth providing a link to the [VCF documentation][1] for future reference on what the fields and terms within the VCF file refer to. [1]: http://samtools.github.io/hts-specs/VCFv4.3.pdf ...
written 4 weeks ago by Russ160
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Comment: C: Tutorials of how the sequencing platform work from beginning to end
... Some of the instrument manufacturers have videos explaining how they work: - [Illumina][1] - [Nanopore][2] - [Pacbio][3] - [IonTorrent][4] edit: oops... just fully read your question and noticed you'd already watched the videos. I'll leave the links up here for others ;) [1]: https://www. ...
written 9 weeks ago by Russ160
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Comment: C: Error while running rnaseq_pipeline.sh provided by hisat2
... I downloaded the files and tested them on my machine; the scripts ran without issue. There must be something in the way your files are organised, or in the edits you made to `rnaseq_pipeline.config.sh`. Perhaps you can try starting fresh by downloading everything into a new directory and maintaining ...
written 9 weeks ago by Russ160
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Comment: C: Error while running rnaseq_pipeline.sh provided by hisat2
... Are you calling the script from the appropriate directory? ...
written 9 weeks ago by Russ160
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Comment: C: Error while running rnaseq_pipeline.sh provided by hisat2
... Check the contents of your script, it looks like the path to your samples is incorrect. Try removing the leading `/` from the samples - this is why the sample file cannot be found, and also why the double `//` is coming up in the last line. ...
written 9 weeks ago by Russ160

Latest awards to Russ

Scholar 7 weeks ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Supporter 9 weeks ago, voted at least 25 times.
Scholar 12 weeks ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]

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