User: Malka

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Malka0
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Posts by Malka

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Download GTF/GFF annotatioon data for NT database, not by organism (for STAR ali
... I see. I do know where my data comes from, but the taxonomy analysis at the above link seems to suggest that that would only be part of the story for any SRA run, with some reads likely aligning with other organisms, whose identity is unknown to me. I want to avoid running a separate alignment on e ...
written 17 days ago by Malka0
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Comment: C: Download GTF/GFF annotatioon data for NT database, not by organism (for STAR ali
... I did, thank you. Specifically because they mention that the software is experimental and the results should be taken 'with a boatload of salt', I am interested in using a different method to arrive at similar results for specific SRA reads. I will look into the packages you mention. Thanks. ...
written 17 days ago by Malka0
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Comment: C: Download GTF/GFF annotatioon data for NT database, not by organism (for STAR ali
... Thanks, I might try your suggestion of running STAR with just FASTA files. I didn't realise that was possible. I will look into it now. Thanks. ...
written 17 days ago by Malka0
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Comment: C: Download GTF/GFF annotatioon data for NT database, not by organism (for STAR ali
... Thanks. I am working on a server which should have enough RAM and memory, and considering working in the cloud too. That way, would it be possible to run STAR alignment against NT? How would I find the necessary annotation files, if yes? Thanks for your advice regarding the other packages. ...
written 19 days ago by Malka0
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Comment: C: Download GTF/GFF annotatioon data for NT database, not by organism (for STAR ali
... Yes, thank you. Specifically because of the disclaimer at the top of the page, I want to use a different tool, which is not experimental... Shouldn't the results be fairly similar regardless of the tool being used? ...
written 19 days ago by Malka0
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Comment: C: Download GTF/GFF annotatioon data for NT database, not by organism (for STAR ali
... Thanks for your fast reply! Please see my comment above (in response to lieven.sterck's answer to my question) as to what I am trying to achieve. Would I not be able to do that by running STAR alignment against NT? Do I understand correctly from your answer that there is no way to run STAR alignme ...
written 19 days ago by Malka0
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Comment: C: Download GTF/GFF annotatioon data for NT database, not by organism (for STAR ali
... Thanks for your fast reply! I want to find out how much of my sequence aligns to each known organism and species. For example, in the Run Browser/Analysis tab in [this][1] link, there's a full Taxonomy Analysis for the particular read. I would like to do basically the same thing, and I thought runn ...
written 19 days ago by Malka0
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Download GTF/GFF annotation data for NT database, not by organism (for STAR alignment)
... Hello, I would like to run some alignments against the full NT database, using STAR. I am having difficulty finding the necessary annotation files for the NT database. I have found GTF/GFF files for specific organisms or species, but not for the full NT database. Where can I find that? Thanks in a ...
alignment next-gen rna-seq written 19 days ago by Malka0

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