User: waqaskhokhar999

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Posts by waqaskhokhar999

<prev • 59 results • page 1 of 6 • next >
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Comment: A: How to run the Deseq2 tool without replicates.
... 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 waqaskhokhar99970
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Filter transcripts based on CDS length
... 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, ...
annotation rna-seq written 11 days ago by waqaskhokhar99970 • updated 11 days ago by Haci120
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Comment: C: Identify transcripts code for longest protein from gene annotation file
... 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 waqaskhokhar99970
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Comment: C: Identify transcripts code for longest protein from gene annotation file
... 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 waqaskhokhar99970
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Identify transcripts code for longest protein from gene annotation file
... 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 ...
reference annotation file rna-seq written 24 days ago by waqaskhokhar99970 • updated 24 days ago by JC8.4k
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Convert intron coordinates to gene names
... 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 ...
sqtl rna-seq written 4 weeks ago by waqaskhokhar99970 • updated 4 weeks ago by Alex Reynolds28k
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Comment: C: Plotting Exons Of A Transcript Using Bioconductor Genomegraphs
... Can we also draw structure of novel transcripts using biomart by adding that information in it? ...
written 6 weeks ago by waqaskhokhar99970
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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 waqaskhokhar99970
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Divide isoform expression by gene expression to calculate splicing ratios
... 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, ...
assembly rna-seq written 11 weeks ago by waqaskhokhar99970
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Comment: C: Increase height of box plots in ggplot
... Many thanks for your suggestion, I have tried violin plots but it also didn't work for me ...
written 11 weeks ago by waqaskhokhar99970

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Popular Question 10 months ago, created a question with more than 1,000 views. For Alternative splicing events in transcriptomic data

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