User: catagui

gravatar for catagui
catagui20
Reputation:
20
Status:
New User
Location:
Miami, FL, USA
Last seen:
6 months, 3 weeks ago
Joined:
4 years, 9 months ago
Email:
c******@gmail.com

PhD student at James Cook University

Posts by catagui

<prev • 15 results • page 1 of 2 • next >
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Comment: C: How To Remove Certain Sequences From A Fasta File
... Hi I tried to use the script but it needs to be updated. I am not an expert so just changed my_seq.tostring() to str() but it is not working.Also does the fasta file needs to have a single line per sample? Message: 'BiopythonDeprecationWarning: This method is obsolete; please use str(my_seq) instead ...
written 7 months ago by catagui20
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Yes I do have 5 genotypes (3 samples per geno) and a control and treatment. ...
written 8 months ago by catagui20
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Comment: C: PCA plot from read count matrix from RNA-Seq
... Hi Kevin sorry for the random question, but would a PCA plot be useful to see the expression of different genotypes to a treatment. I have 5 genotypes and would like to see how the expression of each pair interact in a plot. Thanks ...
written 9 months ago by catagui20
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Comment: C: HISAT2 running pair end
... Thanks, it seems that the program only reads the 1.fq or 2.fq for pair-reads. I wanted to make sure this is the case before editing all my files. ...
written 10 months ago by catagui20
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HISAT2 running pair end
... Hi is my first time to use HISAT2 but it does not want to run. I just get: Warning: Could not open read file "S1_F_paired.fq" for reading; skipping... I understand that by adding -q it should read the .fq files. Do I need to change my files names to 1.fq and 2.fq to each of my sample reads? I have ...
rna-seq hisat2 written 10 months ago by catagui20
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Comment: C: Options for generating proportional Venn Diagram of 4 sets
... Can it generate proportional diagrams? I am using it now, but can not find the proportional option. Thanks ...
written 3.4 years ago by catagui20
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Comment: C: Options for generating proportional Venn Diagram of 4 sets
... Thanks, I didn't know they are not possible to generate 4 set Venn Diagram. Also good to know Cytoscape is a good option at least for the 3 way.  ...
written 3.6 years ago by catagui20
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Options for generating proportional Venn Diagram of 4 sets
... Hi is there any updates on generating proportional Venn diagrams since the below post? https://www.biostars.org/p/7713/#7877 BioVenn (http://www.cmbi.ru.nl/cdd/biovenn/index.php) is useful but I need 4 sets not 3.  I guess R can generate proportional diagrams?  Thanks   ...
R venn diagram rna-seq written 3.6 years ago by catagui20 • updated 3.5 years ago by Nicola Casiraghi440
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Comment: C: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Path
... Thanks for the script Kamil I will try it out.  ...
written 3.7 years ago by catagui20
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Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Pathway code?
... Hi is there a way to get all the fasta protein sequences from one KEGG pathway? I want to get all the sequences from a Nematostella pathway: nve04068   FoxO signaling pathway It would be something similar to this post: https://www.biostars.org/p/3133/#134716 , but not sure it is ...
pathway fasta kegg written 3.7 years ago by catagui20 • updated 3.7 years ago by Kamil1.8k

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