User: hwu12

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hwu1250
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Posts by hwu12

<prev • 23 results • page 1 of 3 • next >
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bed file to gtf/gff
... Hi, I have a bed file with. column 1: chromosome number column 2: exon start column 3: exon stop column 4: gene name column 5: start of coding sequence (CDS) column 6: end of coding sequence (CDS) column 7: strand See below for example. Is there a way to transform it to gtf/gff for ...
genome annotation written 11 weeks ago by hwu1250
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Comment: C: Host bam file on MongoDB?
... If I have a mlab account, can I consider that my server? ...
written 3 months ago by hwu1250
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Comment: C: Host bam file on MongoDB?
... How could I store the BAM on my server if I do not have one? As I said I would not have server access for few months :-( Even I have a server, I think MongoDB is more stable and it is free in some cases. Thanks for the link. I will think about it :-) ...
written 3 months ago by hwu1250
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Comment: C: Host bam file on MongoDB?
... I want to make a shiny app to visualize a unique type of RNAseq results. Some characters of this RNAseq data cannot be visualized with IGV. I do it with R on my Mac (wouldn't have a server for few months), but it would be a lot easier for my collaborators if it is in a shiny app. ...
written 3 months ago by hwu1250
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Host bam file on MongoDB?
... Is it possible to host a bam file on MongoDB and slice it with R? I am thinking to develop a shiny app to visualize RNAseq reads for my data. Thanks! ...
mongodb R written 3 months ago by hwu1250
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Comment: C: Homologs between tomato and Arabidopsis
... Thanks :-) It is just a little sad that the homologs are based on TAIR10 and an older version of Tomato transcriptome. I guess If I want to use the latest version of tomato annotation and Araport 11 annotation, I will have to blast them myself. ...
written 4 months ago by hwu1250
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Comment: C: Homologs between tomato and Arabidopsis
... It seems to me that the orthoDB is for checking few genes. Can we use it to generate a list of all homolog pairs between two species? Thanks! ...
written 4 months ago by hwu1250
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Homologs between tomato and Arabidopsis
... I was wondering if there is a database for the homologs between two plants. Specifically, I am looking for a list of homologs between tomato and Arabidopsis. Thanks! ...
genome homology written 4 months ago by hwu1250 • updated 4 months ago by h.mon9.2k
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Comment: C: Differential expression for two very different samples
... Thanks so much, James! For others interested in this method, a user's guide can be found at https://github.com/stephaniehicks/qsmooth/blob/master/vignettes/qsmooth-vignette.pdf ...
written 4 months ago by hwu1250
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Comment: C: Differential expression for two very different samples
... It is a very good idea to prioritizing genes instead of normalizing genes. Thanks, Michele. ...
written 4 months ago by hwu1250

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