User: hwu12

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hwu1210
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Posts by hwu12

<prev • 20 results • page 2 of 2 • next >
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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 20 months 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 20 months 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 20 months ago by hwu1210 • updated 20 months ago by Michael Lawrence11k
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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 24 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 24 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 24 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 2.0 years 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 2.0 years ago by hwu1210
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Extract isoform-specific ranges
... Hi, is there a way to identify/extract the isoform-specific ranges for multiple isoforms? For example:  GeneA.1 with 1 ranges [1,10] GeneA.2 with two ranges [1,3][8:10] GeneA.3 with two ranges [1,3][7:15] I want: The range specific for GeneA.1 is [4:6] The range specific for GeneA.2 is none T ...
genomicranges bioconductor written 2.0 years ago by hwu1210 • updated 2.0 years ago by Malcolm Cook1.5k
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Generate START and STOP ranges from a gff file
... Hi, I am using the new tomato ITAG3.0 annotation, but the gff file does not contain the rows for the start and stop codon positions. It only contains ranges for "gene", "transcript", "cds", "exon" and "3' UTR" and "5' UTR". Is there a way to fix that? In other words, is there a way to generate a gf ...
annotation gff bioconductor written 2.5 years ago by hwu1210

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