User: LP

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LP20
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New User
Location:
South Africa
Last seen:
2 years, 9 months ago
Joined:
3 years ago
Email:
l*****************@gmail.com

Posts by LP

<prev • 8 results • page 1 of 1 • next >
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Comment: C: phytozome gtf file
... Hi Juke-34, It is very easy and free to register on phytozome - thanks to genomax for providing the link. By registering on phytozome, you will not only access sorghum genome, but also other genomes that may be of interest to you. I really do need someone to show or instruct me how it is done to c ...
written 2.9 years ago by LP20
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Comment: C: phytozome gtf file
... I tried to provide the link, but I failed. The link requires one to have an existing account with phytozome. In other words if you have an account you will be required to login in order to access the gff file (Sbicolor_454_v3.1.1.gene.gff3) from your side. If your are not registered on Phytozome, un ...
written 2.9 years ago by LP20
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Comment: A: phytozome gtf file
... Have you managed to overcome the problem you had with the gtf file created from gff3? Did it finally run successfully? I have the same problem with my sorghum gff3 file. ...
written 3.0 years ago by LP20
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Comment: C: How to Run the Script for Extracting Splice Sites from the Gene Annotation File
... Thanks genomax for your explanation of what "sed" is. So let me try to use it and see what happens. ...
written 3.0 years ago by LP20
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Comment: C: How to Run the Script for Extracting Splice Sites from the Gene Annotation File
... Thanks Renesh and genomax - very much appreciated! ...
written 3.0 years ago by LP20
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Comment: C: How to Run the Script for Extracting Splice Sites from the Gene Annotation File
... Thanks for your input @ george.ry. So how does sed work? Does it mean direct subtitution of "_ID" with "_id". I was intending to just manually replace "_ID" with "_id" hoping the implemented changes would enable the script to work. I haven't done that yet. So I am really not sure what to do right no ...
written 3.0 years ago by LP20
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Answer: A: How to Run the Script for Extracting Splice Sites from the Gene Annotation File
... Thanks guys for your answers - very much appreciated. st.ph.n - to answer your question as to where I got the extract_splice_sites.py, I would say the script comes with the HISAT package. I think it basically helps to improve your mapping. One has to perfom this step although in my opinion performi ...
written 3.0 years ago by LP20
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How to Run the Script for Extracting Splice Sites from the Gene Annotation File
... Hi Biostars Community, I struggle with running the script (extract_splice_sites.py Sbicolor_313_v3.1.gene.gtf > Sbicolor_313_v3.1.splicesites.txt) for extracting the splice sites from my gene annotation file. I was initially advidsed to convert my gene annotation file (Sbicolor_313_v3.1.gff3) to ...
software error alignment rna-seq written 3.0 years ago by LP20

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