User: Tye Kahn

gravatar for Tye Kahn
Tye Kahn10
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10
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New User
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Last seen:
7 months ago
Joined:
3 years, 3 months ago
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j*********@gmail.com

Posts by Tye Kahn

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Differential expression tool that can take TPM as input?
... Already searched for it, but none of the results was informative. About the link, CPM, unlike TPM, does not take gene length into account. Do you think that may have any effect on the results? I would think so. ...
written 7 months ago by Tye Kahn10
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Differential expression tool that can take TPM as input?
... Due to my analysis, I need to use TPM as input for my differential expression analysis. I tried to use both DESeq2 and EdgeR by skipping both normalization and independent filtering steps. Even so, the number of DEGs is 3 times lower than using the original raw data (in DESeq2). Does any of you k ...
differential-expression tpm rna-seq written 7 months ago by Tye Kahn10 • updated 7 months ago by ATpoint36k
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Comment: C: venn plot data?
... Have you tried the examples from the [documentation][1] before using it in your data? If they work, then try to use the same format for your data. [1]: https://cran.r-project.org/web/packages/venn/venn.pdf ...
written 15 months ago by Tye Kahn10
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Comment: C: MapSplice2 circRNA output
... Indeed, looks like it is a parameter in whether one or another are chosen, but not both at the same time; as the --fusion-non-canonical parameter already includes the former results (from --fusion). So if in your case you think that actually, the '--fusion-non-canonical' flag is the adequate one, I ...
written 24 months ago by Tye Kahn10
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Answer: A: Software for Genome Annotation
... I would recommend [this review][1] which was really helpful to me for the genome annotation of a fly's species. I will give you a few tips that I learned from that process: - Remember to first mask repetitive regions, as they may be misannotated as any other genetic elements than that. - Pipel ...
written 2.0 years ago by Tye Kahn10
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Answer: A: genepredtogtf command fails
... I had the same error, and from what I can see, the error comes from the input file. That's because your initial file does not have at least 12 words/columns in all lines, and therefore, after using cut, the resulting words used as input to genePredToGtf are less than 10 (in your case, that happens i ...
written 2.0 years ago by Tye Kahn10
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MAKER AED score
... Hi everyone, I recently have performed a **new genome annotation** with EVM, thanks to *ab initio* predictions, RNA-Seq data and homology protein alignments. As there was an old annotation already, I wanted to analyze the **AED score** from both annotations, which takes into account their accuracy ...
annotation evm aed-score rna-seq maker written 2.9 years ago by Tye Kahn10
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Comment: C: Augustus install mac
... I had a similar error, and in the end, I found a [detailed step-by-step manual][1] to correct this error, which is based on this answer. Edit: After following this manual, it gave me the same error, but at least it seems like I can run the program from the augustus/src/ directory. [1]: https://i ...
written 3.1 years ago by Tye Kahn10
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Comment: C: Convert XML file to FASTA
... In the end I found a site in the same database where the data is included in the desired format, so I didn't need to perform it. Anyway, thanks for your help. ...
written 3.1 years ago by Tye Kahn10
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Comment: C: Convert XML file to FASTA
... Yes, unfortunately, it seems that it only works the other way around, obtaining XML files instead of getting rid of them. ...
written 3.2 years ago by Tye Kahn10

Latest awards to Tye Kahn

Popular Question 15 months ago, created a question with more than 1,000 views. For Convert XML file to FASTA
Popular Question 24 months ago, created a question with more than 1,000 views. For Alternative to GMAP for mapping Trinity transcripts to genome
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Alternative to GMAP for mapping Trinity transcripts to genome

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