User: hwu12

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hwu1210
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Posts by hwu12

<prev • 12 results • page 1 of 2 • next >
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Comment: C: RNAseq analysis: how to compare two very different samples?
... These questions bothered me for a long time. Thanks so much, Aaron. I really appreciate your help.   ...
written 1 day ago by hwu1210
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RNAseq analysis: how to compare two very different samples?
... Hi everyone, I heard that edgeR and DESeq2 assume that most genes in the samples are equally expressed, and only a small fraction of genes are differentially expressed. I was wondering how to compare two very different RNA samples. For example, one from muscle and the other from the liver. I know s ...
rnaseq edger deseq2 written 1 day ago by hwu1210 • updated 1 day ago by Aaron Lun18k
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Comment: C: Generate 3' UTR and 5' UTR ranges from a gff file
... Thanks so much, Michael. This method can efficiently generate UTR ranges. However, is it possible to split them further to 5'UTR and 3'UTR? ...
written 21 days ago by hwu1210
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Comment: C: Generate 3' UTR and 5' UTR ranges from a gff file
... Hi arfranco, could you please be more specific how to use bedtools to get the UTR rows? I spent a lot of time looking, but it seems that bedtools cannot generate the 5'UTR and 3'UTR ranges for me.Thanks!  ...
written 23 days ago by hwu1210
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Generate 3' UTR and 5' UTR ranges from a gff file
... I am working on a gif file that is missing the 5'UTR and 3' UTR information. For example: ​ ctg123 . gene 1050 9000 . + . ID=gene00001;Name=EDEN ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1 ctg123 . exon 1050 1500 . + . ID=exon00002;Par ...
genomicranges gff written 24 days ago by hwu1210 • updated 22 days ago by Michael Lawrence9.8k
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Comment: C: Extract isoform-specific ranges
... Thanks! I uploaded an image to issue #439 from the two browsers to show the problem. Hopefully, they can fix it soon. In any case, I will use the Firefox to vote in the future.  ...
written 4 months ago by hwu1210
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Comment: C: Extract isoform-specific ranges
... The problem is in my Safari browser. I cannot/never see the green circle there. I switched to Firefox and can see it now. Thanks again. ...
written 4 months ago by hwu1210
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Comment: C: Extract isoform-specific ranges
... Malcolm, how can I accept your answer? I want to do it but I cannot find a way to do it. It is not similar to StackOverflow. Sorry I did not see your reply until now. Please let me know and I will accept your answer. Thanks again! ...
written 4 months ago by hwu1210
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Comment: C: Extract isoform-specific ranges
...  Malcolm Cook, thank you so much for the complete example. Michael Lawrence, thanks for your help, too. I really appreciate it. ...
written 4 months ago by hwu1210
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Comment: C: Extract isoform-specific ranges
... Thanks, Michael. I am actually looking for a way to isolate isoform-specific ranges (e.g. for the isoform 1 in the example, the bases from 4 to 6 are unique for the isoform 1 because it is spliced out in other 2 isoforms and does not exist in the final transcript. The [11:15] range for isoform 3 is ...
written 5 months ago by hwu1210

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