User: amy.bashir

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amy.bashir80
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Posts by amy.bashir

<prev • 20 results • page 1 of 2 • next >
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Doing interspecies comparison using publicly deposited RNA-seq data
... Hello! I am currently analyzing the protein-coding transcriptome of a tissue from my organism of interest (non-model organism). I want to see whether I can also study the transcriptomes of this tissue in other species (mouse, fruitfly, zebrafish, etc) using publicly deposited RNA-seq data in NCBI S ...
rna-seq interspecies comparison written 5 months ago by amy.bashir80
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Comment: C: Extracting promoter sequence for reverse/minus strand gene from genome browser
... Great, thank you very much! ...
written 5 months ago by amy.bashir80
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Extracting promoter sequence for reverse/minus strand gene from genome browser
... Hello! I would like to extract the promoter/upstream sequence of a gene from the genome of a non-model organism. The gene is on the reverse strand, as can be seen below, with the region that I am interested in indicated by the red rectangle. ![image][1] If I extract the sequence of this region ...
genome browser promoter reverse strand gene written 5 months ago by amy.bashir80 • updated 3 months ago by Alex Reynolds26k
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BRAKER1 unexpected termination
... Hello everyone! Recently my locally installed BRAKER1 keeps terminating the job unexpectedly, at the “NEXT STEP: run AUGUSTUS” point. I don’t see anything particular in “braker.log”, which just stops at a "run AUGUSTUS for file" step. I have been able to run a complete BRAKER1 job before on smalle ...
braker1 written 12 months ago by amy.bashir80
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Comment: C: Differentiating between stranded and unstranded RNA-seq data by mapping to genom
... Great, thank you very much for the clarification. I did try RSeQC, and got the output: Fraction of reads explained by "1+-,1-+,2++,2--": 0.9803 From what I see around online, this corresponds to a RF library? ...
written 13 months ago by amy.bashir80
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Comment: C: Differentiating between stranded and unstranded RNA-seq data by mapping to genom
... Is it not possible to tell from the information that I provided? ...
written 13 months ago by amy.bashir80
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Differentiating between stranded and unstranded RNA-seq data by mapping to genome
... Hello everyone! I have some paired-end RNA-seq data from a collaborator. I was told that they are "stranded", but nothing about whether it's RF or FR. I pulled out 5 pairs of reads (read 1 and read 2) from each of the four RNA-seq libraries and aligned them to the reference genome of the organism ...
rna-seq written 13 months ago by amy.bashir80 • updated 13 months ago by Friederike2.3k
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Answer: A: Tools for investigating the correlation of differential gene expression & histon
... I think BETA (http://cistrome.org/BETA/) is well suited for this task. ...
written 14 months ago by amy.bashir80
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Answer: A: WGCNA analysis for normalised data expression data sets
... Trait data is biological features associated with each animal that the sample is derived from. For example, if you are studying the gene co-expression networks underlying a cardiovascular disease, trait data would be the things like weight, blood pressure and blood cholesterol level of each patient/ ...
written 14 months ago by amy.bashir80
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Comment: C: Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run
... I will just say up front that I am really new to all this too... Do you have root access on the system you are using, i.e. can you use sudo? Maybe it would be easier to follow the instructions [here][1] to set up a new place where you can use CPANminus to install modules. [1]: https://stack ...
written 14 months ago by amy.bashir80

Latest awards to amy.bashir

Scholar 14 months ago, created an answer that has been accepted. For A: WGCNA analysis for normalised data expression data sets

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