User: Yuka Takemon

gravatar for Yuka Takemon
Yuka Takemon40
Reputation:
40
Status:
New User
Location:
Canada/Vancouver/GenomeSciencesCentre
Last seen:
4 days, 5 hours ago
Joined:
4 years, 10 months ago
Email:
y***********@gmail.com

Posts by Yuka Takemon

<prev • 20 results • page 1 of 2 • next >
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Answer: A: Is it safe to keep our data in github
... Hi Rprog008, Personally, I would never keep data on GitHub and would suggest that you remove your data from GitHub. For the most part, data should be stored on your company/personal server where only you and your colleagues have secured and restricted access to. Especially true with raw data, ther ...
written 5 months ago by Yuka Takemon40
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Comment: C: Issue with DEXSeq installation
... Hi Hussain, I feel very silly that I didn't update my R version before posting. It worked on R 3.4.3. Thank you! ...
written 2.8 years ago by Yuka Takemon40
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Issue with DEXSeq installation
... Hello, I am having issues installing the DEXSeq R package. I updated both bioinstaller and GenomicRanges in order to solve the problem, but no luck. Any insights would be appreciated. Cheers, Yuka > biocLite("DEXSeq") BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (Bi ...
dexseq R bioconductor written 2.8 years ago by Yuka Takemon40 • updated 2.8 years ago by Hussain Ather940
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Comment: C: TopHat --max-multihits interpretation
... Thanks @genomax2 for your response. I understand that read aligned doesn't directly equal FPKM, however if I decrease my --max-multihits, I will then also decrease the number of alignments. Therefore that could also decrease my FPKM? ...
written 3.8 years ago by Yuka Takemon40
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TopHat --max-multihits interpretation
... Hello, I have read some postshere regarding TopHat's --max-multihits option, where and option of 1 will give you the most conservative alignment. However I would like to ask if my following interpretation is correct: If I have the default setting for --max-multihits (default is 20), does that mean ...
tophat rna-seq written 3.8 years ago by Yuka Takemon40
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Comment: C: RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
... Oops you're right Charles. Thanks for correcting me. ...
written 3.8 years ago by Yuka Takemon40
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Answer: A: RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
... 12 months too late but I disagree with @iraun, `Fraction of reads explained by "+-,-+": 0.9817` for a single end sequencing would be unstranded (`fr-unstranded`). If your reads were stranded, a higher percentage would be explained by `"++,--"` . Documentation isn't the clearest, but you can figure ...
written 3.8 years ago by Yuka Takemon40
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Answer: A: TruSeq strand-specificity in rsem-calculate-expression
... I just stumbled upon this while struggling with `rsem` strand directions. Do not simply use `--strand-specifi`c for stranded reads, as you would need to specify direction of the read. If you've used `TopHat` you'll be familiar with parameters such as ` --library-type fr-firststrand`, do not assume ` ...
written 3.8 years ago by Yuka Takemon40 • updated 11 months ago by RamRS30k
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Cuffdiff isoform_exp.diff output: How do you find which isoform TCONS id is referring to?
... Hello! I am analysing RNAseq data using cufflinks/2.2.1 to run cuffdiff for two groups of samples WT vs KO. I am interested in knowing which of the isoforms of a corresponding gene is differentially expressed. test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change ...
transcript_id tcons cufflinks cuffdiff rna-seq written 4.6 years ago by Yuka Takemon40
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Comment: C: Is there a limit to the p-value & q-value for cuffdiff gene_exp.diff?
... Thanks for finding the 2.1.0 release... what a bummer. I guess I will have to learn Kallisto & Sleuth now. ...
written 4.7 years ago by Yuka Takemon40 • updated 9 months ago by RamRS30k

Latest awards to Yuka Takemon

Popular Question 4 months ago, created a question with more than 1,000 views. For Is there a limit to the p-value & q-value for cuffdiff gene_exp.diff?
Supporter 7 months ago, voted at least 25 times.
Popular Question 10 months ago, created a question with more than 1,000 views. For Is there a limit to the p-value & q-value for cuffdiff gene_exp.diff?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For (Closed) How to split Illumina Hiseq 2000 paired-end fastq files?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Is there a limit to the p-value & q-value for cuffdiff gene_exp.diff?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Is there a limit to the p-value & q-value for cuffdiff gene_exp.diff?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Is there a limit to the p-value & q-value for cuffdiff gene_exp.diff?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Cufferge IOError: Errno 2 no such file or directory

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