User: I0110
I0110 • 120
- Reputation:
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- United States
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- 1 month ago
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- 4 years, 10 months ago
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Posts by I0110
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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 14 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 15 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 15 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 15 months ago by
I0110 • 120
• updated
15 months ago by
colindaven • 2.3k
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C: R, plot text table
... This question is not about bioinformatics... ...
written 15 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 2.2 years ago by
I0110 • 120
• updated
2.1 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 2.3 years ago by
I0110 • 120
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C: transition to bioinformatics
... It is not too late for you to learn few programming languages. Learn comment line, python and R will certainly help (and they are not difficult). If you do not get in this year, you can add those skills to your CV and you will most likely to get in next year. Besides the "info" part, bioinformatics ...
written 2.3 years ago by
I0110 • 120
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... Hi Devon, Thanks so much for your help on the bioinformatics stackexchange site. Sorry, I posted on the stackexchange bioinformatics site and waited for a day. Is there a general rule? For example, how long should I wait before I cross-posted? Or I should delete one before I posted in another? Pleas ...
written 2.3 years ago by
I0110 • 120
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