User: Qian Dong

gravatar for Qian Dong
Qian Dong50
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50
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New User
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Last seen:
4 years, 9 months ago
Joined:
5 years, 2 months ago
Email:
d****@umail.iu.edu

Posts by Qian Dong

<prev • 5 results • page 1 of 1 • next >
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Comment: C: How Should I Include Biological Replicates In Cufflink/Cuffdiff?
... Dear Jeremy, Thank you for your advice! However when I tried this out I got some more questions. I am dealing with a bacterium which has about 4000 genes. When I tried Cuffmerge to merge everything with reference annotation, I got a merged file of only 50 lines. If I left out the reference annota ...
written 4.8 years ago by Qian Dong50
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How Should I Include Biological Replicates In Cufflink/Cuffdiff?
... Dear team, I have a few questions regarding RNA-seq data analysis. I want to compare transcriptome profile of a bacterium between 5 time points, and for each time point I have three biological replicates. Right now I have each of the replicates' sequences aligned with Bowtie and assembled transcrip ...
bowtie cufflinks cuffmerge alignment rna-seq written 4.8 years ago by Qian Dong50 • updated 4.8 years ago by Jeremy Goecks2.2k
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Cuffdiff Results Interpretation: High Fold Change But Not Significant
... Dear team, I've been having some problem with cuffdiff results interpretation. I understand that on for a certain sample, it has to have a log2(fold change) that is larger than the cutoff and also have a q-value that smaller than a cutoff. I have a lot of genes that have a really high fold change a ...
cuffdiff rna-seq written 5.2 years ago by Qian Dong50 • updated 2.8 years ago by cmayer0
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Comment: C: Gff Not Recognized In Cufflink
... Dear Jennifer, My .fasta reference genome is like this: '>gi|289546492|ref|NC_011420.2| Rhodospirillum centenum SW chromosome, complete genome' and in the SAM file generated by BOWTIE it says: @SQ SN:gi|289546492|ref|NC_011420.2| LN:4355543 So I think they are all the same as "NC_ ...
written 5.2 years ago by Qian Dong50
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Gff Not Recognized In Cufflink
... Dear Team, I've been having a problem with cufflink regarding GFF files. I tried searching the mailing list first and failed to find an answer. Could you help me look at this? I downloaded my genome annotation GFF file from NCBI (soon I realized NCBI format may be a problem) for my bacterial RNA-s ...
rna-seq cufflinks gff written 5.2 years ago by Qian Dong50 • updated 5.2 years ago by Jennifer Hillman Jackson23k

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