User: camelbbs

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camelbbs610
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China
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Posts by camelbbs

<prev • 178 results • page 1 of 18 • next >
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IRES prediction tool
... Hi all, we want to ask if there is a tool can predict the Internal ribosome entry site (IRES). We have ~200k sequences and using web server is not possible. Any script could be downloaded? Thanks in advance! Cam ...
translation written 3 months ago by camelbbs610
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(Closed) Can Hiseq Xten used for transcriptome sequencing?
... Dear all, We want to ask if Hiseq Xten could be used for transcriptome sequencing. The illumina official said they are not designed for transcriptome seq. So any problems if using this? Thanks a lot, Camel ...
hiseq platform sequencing written 4 months ago by camelbbs610
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how to get the binding motif of splicing factor
... I want to ask if anywhere we can find the binding motif (consensus sequence) of splicing factor or RNA binding proteins. And another, does one RBP only have one binding site? Thanks, Cam ...
rna binding protein written 6 months ago by camelbbs610
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Comment: C: where to download genepattern zip file
... Thanks. But I mean I cannot get the modules online. The download page is down. ...
written 10 months ago by camelbbs610
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where to download genepattern zip file
... Just want to ask if anyone have experience in installing the GenePattern? Seems the online module repository is down. And I don't know where to find the downloadable zip files. Can anyone provide the link? Thanks a lot! ...
genepattern written 10 months ago by camelbbs610 • updated 10 months ago by alaindomissy140
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Comment: C: Number of reads in one gene affect the differential expression analysis?
... Hi agata, I am not sure if cufflinks based on the FPKM or the raw counts. I see the latest version is cuffquant, does it calculate the DE genes based on FPKM? ...
written 13 months ago by camelbbs610
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Comment: C: Number of reads in one gene affect the differential expression analysis?
... Hi i.sudbery, thanks very much for your reply. However, I am not very understand you say "What you absolutely don't want to do is normalise by total library size, as a naïve implementation of FPKM would do". Can I just compare the FPKM to get the differential expressed genes? I thought that is a bet ...
written 13 months ago by camelbbs610
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Comment: C: Number of reads in one gene affect the differential expression analysis?
... Thanks agata, I agree using FPKM is a safe method to calculate the differential expressed genes, especially in this case. ...
written 13 months ago by camelbbs610
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Comment: C: Number of reads in one gene affect the differential expression analysis?
... library is total RNA with rRNA depleted, and strand-specific. HTSeq-count for generating counts. ...
written 13 months ago by camelbbs610
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Number of reads in one gene affect the differential expression analysis?
... Hi all, I recently calculate the differential expressed genes from RNASeq data by DESeq. One question is bothering me. When we checked the number of reads in every gene we annotated, we found some genes have huge number of reads, compare to total reads, such as: sample s-664561 s-665905 s-65 ...
rnaseq counts deseq deg rna-seq written 13 months ago by camelbbs610 • updated 13 months ago by i.sudbery1.6k

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