User: TrentGenomics

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Posts by TrentGenomics

<prev • 40 results • page 1 of 4 • next >
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Comment: C: ABBA-BABA D statistics to pattern introgressed loci: applicable to RNA-seq data?
... Yes, that is correct. The "pure" outgroup is not closer to any of the 4 individuals, but is in the same family (Sciuridae). Thanks, Gabriel. ...
written 6 weeks ago by TrentGenomics30
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Comment: C: ABBA-BABA D statistics to pattern introgressed loci: applicable to RNA-seq data?
... So, I have RNA-seq data from 4 individuals of two evolutionary-young species (two individuals per species). The two species are able to hybridize, and my RNA-seq data was obtained from individuals that were sampled from the hybrid zone which differs in degree of sympatry (ie one individual may have ...
written 7 weeks ago by TrentGenomics30
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ABBA-BABA D statistics to pattern introgressed loci: applicable to RNA-seq data?
... Hello, I'm interested in detecting patterns of introgression across transcriptomes, and was advised to look into D statistics. However, I'm under the impression that these statistics can only be applied to genomes. I have RNA-seq data for closely related species and the corresponding SNPs, and a g ...
rna-seq snp written 7 weeks ago by TrentGenomics30 • updated 7 weeks ago by stolarek.ir550
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Comment: C: Calling de novo SNPs between two species with KisSplice
... No problem! I used a perl script to filter out SNPs of interest. Thanks for getting back to me. ...
written 7 weeks ago by TrentGenomics30
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Answer: A: Calling de novo SNPs between two species with KisSplice
... Is there any sources of script to process the mainOutput.tsv file? Eg. summarizing SNPs based on allele frequencies, read counts, and other important descriptors? I only have a year of bioinformatics experience under my belt, and the learning curve has been steep for me in terms of processing more c ...
written 4 months ago by TrentGenomics30
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Comment: C: Calling de novo SNPs between two species with KisSplice
... Ah yes, that makes sense to me now. A very good explanation, Thank you very much, Vincent. ...
written 4 months ago by TrentGenomics30
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Answer: A: Calling de novo SNPs between two species with KisSplice
... Hi Vincent, Thank you for the detailed explanation, it was extremely useful. Sorry for my misunderstanding, kissDE does suit my needs. I think I am on the right track now. What is the run time of kissDE in your experience? I used kissDE on a cluster previously, and it ran for 10+ days. I was wonde ...
written 4 months ago by TrentGenomics30
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Answer: A: Calling de novo SNPs between two species with KisSplice
... Thanks again for getting back to me so quickly. I'm concerned with finding SNPs between conditions, rather than within a condition. For example, if I consider each of my two species a separate condition (species 1 = cond 1, species 2 = cond 2) , then I would like to find SNPs between those conditio ...
written 5 months ago by TrentGenomics30
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kissDE error during 'diffExpressedVariants' step: "Error in data.frame..."
... Hi, I'm running kissDE on the results obtained from KisSplice. I used 4 paired-end samples as input for KisSplice, with each of the 8 FQ files totaling ~ 13 gigabytes each. Using R on a high performance computer cluster, kissDE ran for ~12 days, before reaching this error during the 'diffExpress ...
R kissde snp kissplice written 5 months ago by TrentGenomics30
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Answer: A: SNPs summaries/statistics from output of KisSplice/KisSplice2RefTranscriptome
... Spent the day learning awk and I think I may be alright with the post analysis. ...
written 5 months ago by TrentGenomics30

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