User: hwu12

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hwu1280
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Posts by hwu12

<prev • 28 results • page 1 of 3 • next >
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Comment: C: The use of "and" in bioinformatics literature
... I really did not know that normalization could be done before log2-transformation. Thanks for sharing the knowledge, Ahill. ...
written 4 days ago by hwu1280
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The use of "and" in bioinformatics literature
... Sorry, this is basically an English problem. I am reading a paper which mentioned they normalized and log2 transformed their microarray data. Does that imply any relationship in time? I meant: did they normalize the data first then log2 transform the data? Thanks! ...
microarray written 4 days ago by hwu1280 • updated 4 days ago by Ahill1.0k
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Comment: C: In gff3 format, could one eukaryotic mRNA contain more than one protein coding s
... Brilliant, mbens! Indeed, "polycistronic" is exactly what I was looking for and should be used for this question. For the gene I have been working on, it is one gene/transcript by annotation, but riboseq data suggests 2 possible ORFs with different peptide sequences. By annotation, it is one gene. I ...
written 18 days ago by hwu1280
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Comment: C: In gff3 format, could one eukaryotic mRNA contain more than one protein coding s
... Hi, mbens, thanks for your help. What I meant is actually: Can one gene/mRNA contains more than one open reading frames? Not CDS. I updated the question. My apologies. ...
written 18 days ago by hwu1280
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In the gff3 format, could one eukaryotic mRNA contain more than one protein coding sequences (i.e. polycistronic)?
... Below is a simple example of gff3 file: 1 T1 gene 3631 4605 . + . ID=ATNG01010 1 T1 mRNA 3631 4605 . + . ID=ATNG01010.1;Parent=ATNG01010 1 T1 exon 3631 3913 . + . ID=ATNG01010:exon:1;Parent=ATNG01010.1 1 T1 CDS 3860 3913 . + 0 ID=ATNG01010:CDS:1;Parent=ATNG01010.1 1 T1 exon 3996 ...
gff3 annotation written 19 days ago by hwu1280
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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 4 months ago by hwu1280
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Comment: C: Host bam file on MongoDB?
... If I have a mlab account, can I consider that my server? ...
written 5 months ago by hwu1280
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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 5 months ago by hwu1280
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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 5 months ago by hwu1280
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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 5 months ago by hwu1280

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