User: I0110
I0110 • 120
- Reputation:
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- United States
- Last seen:
- 2 days, 9 hours ago
- Joined:
- 5 years, 3 months ago
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Posts by I0110
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C: Gene Set Enrichment Analysis
... Above mentioned "the original methodology was designed to work on microarray but later modification made it suitable for RNA-seq also" so I am curious :) ...
written 5 weeks ago by
I0110 • 120
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A: Gene Set Enrichment Analysis
... Thanks for the very nice tutorial. I was wondering what modification needs to be done for a GSEA tool (developed for microarray) to use the RNA-seq data? ...
written 5 weeks ago by
I0110 • 120
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C: Nanopore data to gtf/gff file
... StringTie2 is just released and appears to be a good solution for this problem: https://www.biorxiv.org/content/10.1101/694554v1 ...
written 19 months ago by
I0110 • 120
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C: Nanopore data to gtf/gff file
... Can we use minimap2 to correct the error first and use the bam file output (I believe they should give a bam output) for GMAP GFF3 output mode? But then why we don't just do the minimap2 > stringtie as Devon suggested? Is there an advantage to use GMAP GFF3 output mode? Thanks! ...
written 20 months ago by
I0110 • 120
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C: Nanopore data to gtf/gff file
... Just not sure if the long reads will not be assembled properly since I only used stringTie for illumina reads before. But I will try that first. Thanks! ...
written 20 months ago by
I0110 • 120
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... Hi,
I want to use Nanopore PCR-cDNA sequencing to detect known and novel isoforms in Arabidopsis under certain growth conditions. I am thinking to use minimap2 for mapping, alignment and error correction. If I want to get a gtf or gff from the mapped long reads, which software should I use? Or does ...
written 20 months ago by
I0110 • 120
• updated
20 months ago by
colindaven • 2.6k
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C: R, plot text table
... This question is not about bioinformatics... ...
written 20 months ago by
I0110 • 120
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... Hi,
I have some RNA-sequencing data and transcriptome assembly for a non-model species. I would like to start a jbrowse to share the information with people interested in this species. I assume that I would need a website with enough space and computation power, but I have no idea how to start. Sho ...
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... I was wondering if there is an easy way to merge mgf (mass-spec) files with Python and Bioconductor. Thanks!!! ...
written 2.6 years ago by
I0110 • 120
• updated
2.6 years ago by
mobiusklein • 160
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... I will certainly add a link and wait for at least one business day next time. Thanks so much for your help, Devon! ...
written 2.7 years ago by
I0110 • 120
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