User: I0110

gravatar for I0110
I0110120
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120
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United States
Last seen:
5 months, 1 week ago
Joined:
4 years, 3 months ago
Email:
h****@ncsu.edu

Posts by I0110

<prev • 46 results • page 1 of 5 • next >
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Comment: 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 7 months ago by I0110120
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Comment: 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 7 months ago by I0110120
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Comment: 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 8 months ago by I0110120
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Nanopore data to gtf/gff file
... 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 ...
assembly sequencing written 8 months ago by I0110120 • updated 7 months ago by colindaven1.9k
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Comment: C: R, plot text table
... This question is not about bioinformatics... ...
written 8 months ago by I0110120
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How to start a website with jbrowse to show sequencing data?
... 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 ...
jbrowse written 16 months ago by I0110120 • updated 16 months ago by Biostar ♦♦ 20
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How to merge mgf files?
... I was wondering if there is an easy way to merge mgf (mass-spec) files with Python and Bioconductor. Thanks!!! ...
proteomics written 18 months ago by I0110120 • updated 18 months ago by mobiusklein160
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Comment: C: What is "Possible polymerase run-on fragment"?
... I will certainly add a link and wait for at least one business day next time. Thanks so much for your help, Devon! ...
written 20 months ago by I0110120
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Comment: 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 20 months ago by I0110120
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Comment: C: What is "Possible polymerase run-on fragment"?
... 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 20 months ago by I0110120

Latest awards to I0110

Popular Question 6 months ago, created a question with more than 1,000 views. For r for RNA/RNA hybrid free energy
Popular Question 10 months ago, created a question with more than 1,000 views. For r for RNA/RNA hybrid free energy
Popular Question 11 months ago, created a question with more than 1,000 views. For How to add the start and stop position information to a gff file?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to add the start and stop position information to a gff file?
Student 14 months ago, asked a question with at least 3 up-votes. For Differential expression for two very different samples
Supporter 20 months ago, voted at least 25 times.

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