User: I0110

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I0110120
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Posts by I0110

<prev • 48 results • page 1 of 5 • next >
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Comment: 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 I0110120
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Comment: 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 I0110120
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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 19 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 20 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 20 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 20 months ago by I0110120 • updated 20 months ago by colindaven2.6k
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Comment: C: R, plot text table
... This question is not about bioinformatics... ...
written 20 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 2.4 years ago by I0110120 • updated 2.4 years 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 2.6 years ago by I0110120 • updated 2.6 years 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 2.7 years ago by I0110120

Latest awards to I0110

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Host bam file on MongoDB?
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