User: tanya_fiskur

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tanya_fiskur30
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Posts by tanya_fiskur

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Salmon or Kallisto without reference transcriptome - possible?
... Hello everyone, Do I understand it correctly that if I want to count reads on a transcript level, and have only the mapped Illumina reads and a .gtf annotation file, I cannot use the Salmon or Kallisto? What could you recommend to use for this purpose? Thank you! ...
next-gen written 8 days ago by tanya_fiskur30 • updated 8 days ago by swbarnes28.1k
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Comment: C: Is it possible to remove unwanted tissue contamination in transcriptome analysis
... Yes, by GO and by the abundance of muscular myozin and troponin genes among the differentially expressed genes. On the MDS there are signs of batch effect (it looks like this: https://ibb.co/yPWsRFz ). Actually, the samples seem to be quite equally contaminated, if I compare the normalized counts of ...
written 10 days ago by tanya_fiskur30
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Is it possible to remove unwanted tissue contamination in transcriptome analysis?
... Hello everyone. I work with brain sample transcriptome which seems to be contaminated with muscular tissue. It was not my fault, and I also cannot re-do the sequencing. I want to do the differential expression analysis, but, of course, part of the "differentially expressed" genes are just a reflect ...
next-gen rna written 10 days ago by tanya_fiskur30
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Comment: C: Is it possible to pool the paired-end data?
... Thank you! I will try to. ...
written 8 weeks ago by tanya_fiskur30
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Is it possible to pool the paired-end data?
... Hello everyone. I have a paired-end dataset and want to pool it to map all reads altogether. I couldn't find the tool which can be used for it. Any suggestions? Thanks a lot in advance! ...
rna-seq written 8 weeks ago by tanya_fiskur30
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Comment: C: How to adjust FDR in plotMD?
... No, it's just EdgeR results after Featurecounts. ...
written 10 weeks ago by tanya_fiskur30
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Comment: C: How to adjust FDR in plotMD?
... Kevin, thank you very much! You helped me many times already :). I tried, but by now it looks like this: https://ibb.co/Ws9Xr4r ![something strange][1] [1]: https://ibb.co/Ws9Xr4r ...
written 10 weeks ago by tanya_fiskur30
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How to adjust FDR in plotMD?
... Hi everyone. Is it possible to adjust FDR in plotMD? There is no such function in the command description (https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/plotMD ), but it's quite necessary. Thanks for any help! ...
rna-seq written 11 weeks ago by tanya_fiskur30 • updated 11 weeks ago by Kevin Blighe63k
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Comment: C: "Enhanced Volcano" package - how to set p adjusted cut off?
... Yes, I saw it, but it's not adjusted p value. It would be too strict, if 10e-6 was a usual FDR :) ...
written 11 weeks ago by tanya_fiskur30
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"Enhanced Volcano" package - how to set p adjusted cut off?
... Hello everyone! There is a nice package, Enchanced Volcano, for plotting differential expression analysis results. There is a way to set pCutoff and FCcutoff. Is it possible to set p adjusted cutoff? Thank you! ...
R differential expression written 11 weeks ago by tanya_fiskur30 • updated 11 weeks ago by Kevin Blighe63k

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