User: waqaskhokhar999
waqaskhokhar999 • 70
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Posts by waqaskhokhar999
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... Its better to use [EdgeR][1] for data without replicates. Please see the section 2.11 (What to do if you have no replicates)
[1]: https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf ...
written 11 days ago by
waqaskhokhar999 • 70
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... I have a large file contains genome annotation information of Arabidopsis thaliana obtained via [Biomart][1]. I want to extract transcripts and corresponding information which have highest CDS length (means those transcripts which codes for longest proteins). The file contains 34 columns and n rows, ...
written 11 days ago by
waqaskhokhar999 • 70
• updated
11 days ago by
Haci • 120
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... Longest transcript doesn't mean it codes for longest protein as it can aslo contain retained introns or part of introns, how can i get the idea of longest protein coding transcript? ...
written 24 days ago by
waqaskhokhar999 • 70
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... I am amble to select the protein coding transcripts but how I can select the transcrip that codes for longest protein?
Seondly if multiple transcipts of variable length code for protein of similar length then which transcript should I need to select? For example gene ([AT2G27490][1]) conatin 4 trans ...
written 24 days ago by
waqaskhokhar999 • 70
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... I have reference annotation file of Arabidopsis thaliana and I am interested to identify extract transcipts that code for longest protein isoform and then extract coodinates of that transcript. Forexample gene (AT1G01020) contain 6 transcripts (AT1G01020.1, AT1G01020.2, AT1G01020.3, AT1G01020.4, AT1 ...
written 24 days ago by
waqaskhokhar999 • 70
• updated
24 days ago by
JC ♦ 8.4k
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... I have a huge list of intron coordinates present in the Arabidopsis thaliana genome, I want to get the gene names based on intron coordinates.
Sampe itron coordinates:
chr start end
1 20259962 20260494
1 20634981 20635060
1 18880866 18881011
Desired output:
chr start end Nam ...
written 4 weeks ago by
waqaskhokhar999 • 70
• updated
4 weeks ago by
Alex Reynolds ♦ 28k
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... Can we also draw structure of novel transcripts using biomart by adding that information in it? ...
written 6 weeks ago by
waqaskhokhar999 • 70
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Comment:
C: Overlap between ranges
... Many thanks for your efforts, is it possible to place the matching rows from file_2 exactly in front of matching rows of file_1, currently its pasting all rows from file_1 and matched rows from file_2 ...
written 10 weeks ago by
waqaskhokhar999 • 70
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... I have a large tab separated matrix containing FPKM values (expression) of known and novel genes and transcripts. The code first needs to calculate overall FPKM for a gene and then divide each isoform FPKM by overall gene FPKM. For example below MSTRG.1 gene contains three transcripts (AT1G01010.1, ...
written 11 weeks ago by
waqaskhokhar999 • 70
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... Many thanks for your suggestion, I have tried violin plots but it also didn't work for me ...
written 11 weeks ago by
waqaskhokhar999 • 70
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For Alternative splicing events in transcriptomic data
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