User: justinfanyi

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Posts by justinfanyi

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Comment: A: Mapping microRNA reads to Genome and non-coding RNAs
... Hey, do you mind sharing any informations you got so far about your questions!..any leads to solve the problem? Thanks ...
written 4.0 years ago by justinfanyi0
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Answer: A: DESEQ multifactor specific sample differentials
... "ADD REPLY" and "ADD COMMENT" buttons are in active with working (link) forwarding to (add your answer), anyway thanks a lot for your insights, I will consider doing away with multifactor altogether then do pairwise! because my previous attempt of row names as design failed(> results = nbinomTest ...
written 4.2 years ago by justinfanyi0
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Comment: A: DESEQ multifactor specific sample differentials
... Thanks Devon, the results I got is still the same after adding species!! > results = nbinomTest(cds, "A", "B") Error in if (dispTable(cds)[condA] == "blind" || dispTable(cds)[condB] ==  :   missing value where TRUE/FALSE needed > design       infection time species A_T24 Treatment   24       ...
written 4.2 years ago by justinfanyi0
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Comment: A: DESEQ multifactor specific sample differentials
... Thanks for your quick response,perhaps have not made my question clear!I want to get DEG for specific samples against control (A) on particular time(24/48) after treatment.The samples(A_T24) for example is species of rice,the rest the same but from different species. > design       infection tim ...
written 4.2 years ago by justinfanyi0
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Comment: A: DESEQ multifactor specific sample differentials
... Thanks Devon for your invaluable advice, All species are included in the design,just highlighted some because of space; I tried subset cds  but i got the follow error: > results = nbinomTest(cds, "A_T24", "B_T24") Error in if (dispTable(cds)[condA] == "blind" || dispTable(cds)[condB] ==  :   mi ...
written 4.2 years ago by justinfanyi0
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DESEQ multifactor specific sample differentials
... I have multifactor deseq design analysis (24 samples in total), without replicates (unfortunately), the collaborators however are aware about the confidence of the results but they are ready to do q-PCR of the highest and lowest fold changes counts from the deseq to validate since money has already ...
deseq2 rna-seq written 4.2 years ago by justinfanyi0
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Comment: C: RNA-seq for ncRNA analysis in Rice
... Thanks Manu, have been trying to find more resources on analyzing all plants ncRNA molecules invain..mean while like you say will start with http://www.biomedcentral.com/1471-2105/13/331/figure/F1...if u come across more precise articles published don`t hesitate to update me. ...
written 4.4 years ago by justinfanyi0
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RNA-seq for ncRNA analysis in Rice
... Could anyone kindly suggest some protocols on analyzing ncRNA using RNA-seq data, articles published on identifying and analyzing Plants ncRNA will be equally of great help. Thanks   ...
next-gen rna-seq blast sequencing written 4.4 years ago by justinfanyi0 • updated 20 months ago by Biostar ♦♦ 20
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Comment: C: Obtaining Aa Position From Snpeff Output:
... How would you extract that field (1300V)only? ...
written 4.6 years ago by justinfanyi0
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Comment: C: SNP plotting from VCF file in (non database) organism
... Thanks for your replies,edited the question to show my intentions of the plotting! ...
written 4.6 years ago by justinfanyi0

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