User: Russ

gravatar for Russ
Russ90
Reputation:
90
Status:
Trusted
Location:
Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
Last seen:
an hour ago
Joined:
2 years, 3 months ago
Email:
r*******@uoguelph.ca

Posts by Russ

<prev • 13 results • page 1 of 2 • next >
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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 8 days ago by Russ90
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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 8 days ago by Russ90
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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 days ago by Russ90
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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 10 days ago by Russ90
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Comment: C: how to extract DP for individuals from the same population and save them in a fi
... You can wrap your commands into a bash `for` loop. For the commands I gave, you could do something like: for x in {1..26}; do java -jar GenomeAnalysisTK.jar -T SelectVariant -sf pop"$x"_inds -V file.vcf -o pop"$x".vcf; java -jar GenomeAnalysisTK.jar -T VariantsToTable -gf DP -V pop"$x".vcf -o p ...
written 19 days ago by Russ90
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Answer: A: how to extract DP for individuals from the same population and save them in a fi
... You could subset your original VCF file into 26 pop_X.vcf files (pop_1.vcf, pop_2.vcf, etc) using GATK [SelectVariants][1]: java -jar GenomeAnalysisTK.jar -T SelectVariants -sf -V original.vcf -o pop_1.vcf and then use GATK [VariantsToTable][2]: java -jar GenomeAnalysisTK.jar -T Variants ...
written 20 days ago by Russ90
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Answer: A: Does the insert size affect the result of the illumina sequencing?
... I think optimal insert size depends partly on the experimental design/objectives and sequencing chemistry used (e.g. MiSeq v3 PE 600 would be different than HiSeq PE 200), and partly due to clustering efficiencies. It doesn't _have_ to be 300-400 bp, but that might be the optimal range for the seque ...
written 21 days ago by Russ90
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Comment: C: fastq to fastq.gz conversion for using HISAT2
... I don't think `HISAT2` requires files to be compressed - it can handle regular fastq files just fine. ...
written 23 days ago by Russ90
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Answer: A: How I get mRNA accession no if I have gene name and location with the help of pe
... If I understand your question correctly, you should be able to use [BioMart][1] on Ensembl: 1. Select the "Ensembl Genes 90" database and then choose your organism (provided it is in Ensembl). 2. In the sidebar, select "Filters". 3. In the main window, expand the "GENE" box and select "Input e ...
written 28 days ago by Russ90
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Answer: C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
... I think the issue is not in your file but in your `stringtie` command. It looks like it could use a bit of tweaking. The `-x` option requires a parameter and is interpreting the `-C hg38.GTF` as input, resulting in the error message. Try removing the `-x` (or specifying a file) and seeing if that he ...
written 29 days ago by Russ90

Latest awards to Russ

Supporter 8 days ago, voted at least 25 times.
Scholar 29 days ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Teacher 29 days 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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