User: andrew.j.skelton73
andrew.j.skelton73 • 3.5k
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Posts by andrew.j.skelton73
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... Consider asking this on the biology stack exchange site ...
written 1 day ago by
andrew.j.skelton73 • 3.5k
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Comment:
C: Cis- eQTL Question
... I don't see the point in reinventing the wheel. Your logic sounds fine, but typically cis distances are around 1e6 bases. Take a look at the matrixEQTL source if you're doing this in R, applying these operations one by one will take forever, but if you can get your head around the matrix operations, ...
written 1 day ago by
andrew.j.skelton73 • 3.5k
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Answer:
A: Cis- eQTL Question
... I'd highly recommend [MatrixEQTL][1], it's phenomenally quick for the scale of tests you're describing. Follow the tutorial, once you've got your head around it, it should be relatively simple to apply to your data.
[1]: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/ ...
written 2 days ago by
andrew.j.skelton73 • 3.5k
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... If you want to use a transcriptome assembler, I think you'd be much safer using [Stringtie][1], as Tophat2 + Cufflinks are in low support / deprecated. There's a method for making these results compatible with DESeq2 / edgeR, see the section "Using StringTie with DESeq2 and edgeR" on that link.
...
written 2 days ago by
andrew.j.skelton73 • 3.5k
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Comment:
C: Kallisto pseudobam to IGV
... I've updated my answer ...
written 2 days ago by
andrew.j.skelton73 • 3.5k
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Answer:
A: Kallisto pseudobam to IGV
... Per @Devon's answer [here][1], you can use samtools to sort your SAM and convert it to BAM.
samtools view -u alignment.sam | samtools sort -@ 4 - output_prefix
Edit: The question is referring to transcriptomic vs genomic mappings for IGV
There's a python script available [here][2] found in [ ...
written 3 days ago by
andrew.j.skelton73 • 3.5k
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... Isn't there a syntax problem here? I thought that GATK's filter expressions couldn't take integers, and they needed doubles, otherwise it'd throw an error.
It should be:
--filterExpression "MQ > 20.0" ...
written 3 days ago by
andrew.j.skelton73 • 3.5k
2
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1
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Answer:
A: Transcripts read count
... Check out [Kallisto][1] -> [Sleuth][2] or [Salmon][3] -> [Wasabi][4] -> [Sleuth][5] for modern differential transcript expression solutions.
[1]: https://pachterlab.github.io/kallisto/about
[2]: https://pachterlab.github.io/sleuth/about
[3]: https://combine-lab.github.io/salmon/
...
written 7 days ago by
andrew.j.skelton73 • 3.5k
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... I've not tested it's effect in DESeq2 to be honest, but I did notice the other day when looking through the tximport package, that there's a parameter called varReduce, which I think uses the bootstraps. You'll be fine not using bootstraps. ...
written 9 days ago by
andrew.j.skelton73 • 3.5k
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159
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... If you make a VCF for each run of the Haplotype Caller (i.e. each sample), then you can combine them to a multisample VCF using VCF-tools ...
written 9 days ago by
andrew.j.skelton73 • 3.5k
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