User: predeus

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predeus1.4k
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Posts by predeus

<prev • 171 results • page 1 of 18 • next >
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Comment: C: Heatmap from the RNAseq raw count data
... If you have a simple text file with your locus tag annotation, you can easily annotate all genes. ...
written 7 weeks ago by predeus1.4k
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Answer: A: Heatmap from the RNAseq raw count data
... You can use an online tool like Phantasus: http://genome.ifmo.ru/phantasus-dev/ there are normalization and other options, and you don't need to have any experience in programming. Tutorial is here: http://genome.ifmo.ru/phantasus-dev/phantasus-tutorial.html ...
written 7 weeks ago by predeus1.4k
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Comment: C: Get GEO microarray probe sequences by GPL ID
... Thank you. I've looked at `biomaRt` (and used it quite a few times) before - they seem to have only the most popular microarray platforms (about 30 different ones for human). If you look at GPLs in GEO, there is over 1000 for each human and mouse. Plus there doesn't seem to be an easy way to match ...
written 9 weeks ago by predeus1.4k
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Comment: C: Get GEO microarray probe sequences by GPL ID
... There are sometimes "annot" tables, and always the "soft" files. Both contain an annotation table, which varies widely between platforms - very few have actual probe sequences. ...
written 9 weeks ago by predeus1.4k
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Get GEO microarray probe sequences by GPL ID
... Hello all, I was wondering if there is a straightforward way to obtain probe sequences for a microarray platform given the GPL ID. I know that there are varying degrees of annotation for microarrays in GEO - most popular ones have "annot" files, while others have "miniml" and "soft" files. However ...
geo microarray gene expression omnibus written 10 weeks ago by predeus1.4k
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Comment: A: 16S-specific multiple alignment of rDNA sequences
... Thank you for all suggestions - extremely useful! ...
written 3 months ago by predeus1.4k
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16S-specific multiple alignment of rDNA sequences
... Hello all, this is a strange question perhaps, but it's brought on by a reviewer to one of my papers. We have used `mafft` to generate multiple sequence alignment for a simple phylogenetic analysis. However, the reviewer suggested we use "method that takes secondary structure of 16S" into account. ...
multiple alignment 16s multiple sequence alignment written 3 months ago by predeus1.4k
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Comment: C: makeblastdb Fasta file with 25 sequences gives Error: mdb_env_open: There is no
... That's interesting info, thank you. What is the difference in e-value calculation - can you point me to where it's described? Would hit ranking still be preserved? ...
written 3 months ago by predeus1.4k
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Comment: C: makeblastdb Fasta file with 25 sequences gives Error: mdb_env_open: There is no
... This seems to be a Win 10 - specific bug. I still have Windows 8 and latest blast works fine on my computer, but my wife with Windows 10 couldn't get it to work. Old version did the trick though. ...
written 3 months ago by predeus1.4k
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Comment: C: makeblastdb Fasta file with 25 sequences gives Error: mdb_env_open: There is no
... did blast algorithm change in any substantial way since 2015? I think it was already very, very established by then - so there should be no difference whatsoever in the main components. ...
written 3 months ago by predeus1.4k

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