User: amy.bashir

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amy.bashir60
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Posts by amy.bashir

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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 weeks ago by amy.bashir60
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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 12 weeks ago by amy.bashir60
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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 3 months ago by amy.bashir60
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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 3 months ago by amy.bashir60 • updated 3 months ago by Friederike930
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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 4 months ago by amy.bashir60
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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 4 months ago by amy.bashir60
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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 4 months ago by amy.bashir60
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Answer: A: Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run
... I remember having a similar problem, it was because I had two versions of Perl installed so the paths got all messed up. Is the Statistics/Descriptive module in one of the paths listed in @INC: /usr/local/lib64/perl5 OR /usr/local/share/perl5 OR /usr/lib64/perl5/vendor_perl OR /usr/share/perl5/ve ...
written 4 months ago by amy.bashir60
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hello, As you recommended, I tried this command to prepare the goa_uniprot_all database: nohup ./prepare_database -db=GO_all -org=goa_uniprot_all & I also tried to use "update" mode along with a gene list, but in both cases, I see that the database files get stuck in the state as shown i ...
written 4 months ago by amy.bashir60
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Comment: C: Are TPM values generated by different programs comparable?
... Oh, that's a great idea. Thank you very much! ...
written 4 months ago by amy.bashir60

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Scholar 4 months ago, created an answer that has been accepted. For A: WGCNA analysis for normalised data expression data sets

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