User: camelbbs

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camelbbs670
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Posts by camelbbs

<prev • 179 results • page 1 of 18 • next >
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Does MetDiff support paired-end reads input?
... Hi all, Does anyone have idea when using MeTDiff to compare m6A abundance between samples? Seems in paper MeTDiff only support single-read input, but MeTPeaks support paired-end input. So I want to compare m6A abundance between samples which sequenced by paired-end reads, how to do that. Thanks, ...
metdiff metpeaks m6a written 19 months ago by camelbbs670
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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 it is inconvenient using web server. Any script could be downloaded? Thanks in advance! Cam ...
translation written 3.1 years ago by camelbbs670 • updated 4 months ago by Biostar ♦♦ 20
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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 3.1 years ago by camelbbs670
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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 3.2 years ago by camelbbs670
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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 3.6 years ago by camelbbs670
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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 3.6 years ago by camelbbs670 • updated 3.6 years ago by alaindomissy160
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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 3.9 years ago by camelbbs670
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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 3.9 years ago by camelbbs670
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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 3.9 years ago by camelbbs670
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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 3.9 years ago by camelbbs670

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