User: 402374688

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40237468820
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Posts by 402374688

<prev • 21 results • page 1 of 3 • next >
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How to import RSEM results to DESeq2 for differential analysis
... The results of RSEM are expected counts of transcripts and genes and they are not integer. DESeq2, however, need a matrix of integer as input. The manual of RSEM said the results of RSEM can be used by DESeq. So my question is how to import non-integer RSEM counts to DESeq2 for downstream differenti ...
deseq2 rsem written 2.1 years ago by 40237468820 • updated 2.1 years ago by Michael Love1.9k
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how to download immune genes from http://cegg.unige.ch/Insecta/immunodb
... I want to identify immune genes in a newly sequenced genome using immune genes of different pathways in fruit fly and mosquitoes as queries. But no direct links are available for me to download from the website "http://cegg.unige.ch/Insecta/immunodb". So could you tell me how I can get these sequenc ...
sequence written 2.6 years ago by 40237468820
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cummRbund error dealing with cuffdiff results
... After I ran cuffdiff and got the DE results, I was trying to visualize the results with cummeRbund package. When I ran the following commands, errors occurred. Typically it was normal and worked well without the replicates=T parameter, but when added some errors just came out. How can I fix this? T ...
software error R cummerbund rna-seq written 2.9 years ago by 40237468820
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trimAl error: the symbol 'B' accesing the matrix is not defined in this object
... I use trimAl to trim MSA file, and the alignment file contains B which is a combination of Asp and Asn. So the trimAl report an error: the symbol 'B' accesing the matrix is not defined in this object. How can I fix this error? Thank you. ...
alignment written 3.1 years ago by 40237468820
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Comment: C: gene synteny analysis without chromosome information
... Unfortunatly no. All my three insects are recently sequenced. I just want to find if there is some synteny regions with scaffold information or rearrangement to genes I mentioned above. ...
written 3.1 years ago by 40237468820
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Comment: C: gene synteny analysis without chromosome information
... Thank you. It's really helpful. In addition, I wanna know since I've got certain gene locations present in all three species, is there some tools that can directly show the relationship of these genes in three insects? ...
written 3.1 years ago by 40237468820
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Comment: C: gene synteny analysis without chromosome information
... Since these three insects don't have chromsome information, can I directly align the assembled scaffolds to obtain synteny blocks? ...
written 3.1 years ago by 40237468820
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Comment: C: Is there some convenient tools that can predict insect-virus protein-protein int
... Thank you. Have you ever tested on insect-virus interaction and can it be used to predict protein-protein interaction between virus and host de novo? ...
written 3.1 years ago by 40237468820
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gene synteny analysis without chromosome information
... Recently we sequenced a genome of an insect. To examine the quality og the genome with related species, we aim to compare synteny relationship among them. I have obtained single copy orthologs that are present in all three insects. I want to know how to show this relationship, some kinds of circular ...
genome synteny written 3.1 years ago by 40237468820 • updated 3.1 years ago by Jean-Karim Heriche21k
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Comment: C: genome-guided transcriptome mapping, genome or gene set?
... Sorry but what is it used for? ...
written 3.4 years ago by 40237468820

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