User: Kanne

gravatar for Kanne
Kanne430
Reputation:
430
Status:
Trusted
Location:
Australia
Last seen:
2 years, 3 months ago
Joined:
8 years, 4 months ago
Email:
k********@gmail.com

Postdoctoral bioinformatician in molecular biology lab.

Posts by Kanne

<prev • 9 results • page 1 of 1 • next >
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Answer: A: circRNA- seq normalization
... If your data is from (rRNA-depleted) total RNA and your read lengths and library fragment lengths are the same between the samples you are comparing, then tags per million is an option but this is pretty crude; the suggestion by Vivek Bhardwaj to use the normalisation values from EdgeR/etc is also a ...
written 3.5 years ago by Kanne430
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Answer: A: Running Cuffmerge error "duplicate/invalid 'transcript' "
... For the record, had your error ("GFF Error: duplicate/invalid 'transcript' feature ID=") and was searching all over the internet and couldn't find the answer. For me, it turned out to be that there was nothing wrong with my reference gtf (which was iGenomes UCSSC hg19). I am fairly sure the proble ...
written 4.5 years ago by Kanne430
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Answer: A: Does Tophat Use The Library-Type Information For Mapping, Or Just For The Xs Fla
... I understand your confusion and this this thought just occurred to me. I haven't spent very long thinking about it so maybe I'm forgetting something but here's a suggestion anyway: Tophat is a spliced read aligner. If you do not supply -G then it will still align reads over splicing junctions, it ...
written 6.6 years ago by Kanne430
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Answer: A: Is Tophat The Only Mapper To Consider For Rna-Seq Data?
... I suspect the reason articles/papers/etc were saying that you should use Tophat is because it is a spliced read aligner which is a critical feature when aligning RNA-seq reads to a reference genome (Spliced Read Aligner means that it maps reads over exon/intron junctions). There are other aligners ...
written 7.2 years ago by Kanne430
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Answer: A: Tophat Junctions.Bed File
... I don't know how long ago you posted this but here's my answer anyhow. As you mentioned, the coordinates from IGV are: left: 1030; right: 2032 And the junctions.bed file contains: rpl3 990 2099 JUNC00001560 872 + 990 2099 255,0,0 2 40,67 0,1042 The coordina ...
written 7.2 years ago by Kanne430
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Answer: A: Bwa Aligner: How To Get Percentage Of Reads Aligned?
... This is the long way 'round, I know, but I usually extract the unmapped reads using a perl script which compares the alignment file to the input read file. I then count the number of lines (wc -l) on the input read file and unmapped read file (of course, dividing by 4 for fastq files). The script I ...
written 8.3 years ago by Kanne430
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Comment: C: Clustering Data (Rna-Seq) Using R To Produce A Heatmap
... True, will do, thanks! ...
written 8.4 years ago by Kanne430
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Comment: C: Clustering Data (Rna-Seq) Using R To Produce A Heatmap
... Wow, good point! Thanks a lot, especially for the code, that is very helpful!! ...
written 8.4 years ago by Kanne430
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17 follow
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Clustering Data (Rna-Seq) Using R To Produce A Heatmap
... I have RNA-seq data (FPKMs) from Cufflinks and would like to cluster it by gene and produce a heatmap. This is my first try at using R and I have spent a LOT of time pouring over the manual/help pages and internet tutorials on how to do this. I can now produce heatmaps using "heatmap" easily enoug ...
gene R rna clustering heatmap written 8.4 years ago by Kanne430 • updated 5.0 years ago by Bohdan Khomtchouk320

Latest awards to Kanne

Scholar 3.5 years ago, created an answer that has been accepted. For A: Running Cuffmerge error "duplicate/invalid 'transcript' "
Appreciated 4.4 years ago, created a post with more than 5 votes. For A: Tophat Junctions.Bed File
Scholar 4.5 years ago, created an answer that has been accepted. For A: Running Cuffmerge error "duplicate/invalid 'transcript' "
Appreciated 6.6 years ago, created a post with more than 5 votes. For A: Is Tophat The Only Mapper To Consider For Rna-Seq Data?
Appreciated 6.6 years ago, created a post with more than 5 votes. For Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Great Question 6.6 years ago, created a question with more than 5,000 views. For Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Librarian 6.6 years ago, created a post with more than 10 bookmarks. For Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Good Question 6.6 years ago, asked a question that was upvoted at least 5 times. For Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Good Answer 6.6 years ago, created an answer that was upvoted at least 5 times. For A: Is Tophat The Only Mapper To Consider For Rna-Seq Data?
Epic Question 6.6 years ago, created a question with more than 10,000 views. For Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: Tophat Junctions.Bed File
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: Is Tophat The Only Mapper To Consider For Rna-Seq Data?
Student 6.6 years ago, asked a question with at least 3 up-votes. For Clustering Data (Rna-Seq) Using R To Produce A Heatmap

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