User: tanya_fiskur

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tanya_fiskur40
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Posts by tanya_fiskur

<prev • 52 results • page 1 of 6 • next >
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Comment: C: How to visualize skipped exon?
... It is from killifish n.furzeri ...
written 5 months ago by tanya_fiskur40
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How to visualize skipped exon?
... Hello! I have two transcripts, and in one of them exon #7 is skipped. I really wish to visualize it. Is there any tool that can help me? Thank you a lot in advance! ...
next-gen alternative splicing written 5 months ago by tanya_fiskur40 • updated 5 months ago by GenoMax94k
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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 5 months ago by tanya_fiskur40 • updated 5 months ago by swbarnes29.4k
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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 5 months ago by tanya_fiskur40
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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 6 months ago by tanya_fiskur40
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Comment: C: Is it possible to pool the paired-end data?
... Thank you! I will try to. ...
written 7 months ago by tanya_fiskur40
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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 7 months ago by tanya_fiskur40
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Comment: C: How to adjust FDR in plotMD?
... No, it's just EdgeR results after Featurecounts. ...
written 8 months ago by tanya_fiskur40
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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 8 months ago by tanya_fiskur40
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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 8 months ago by tanya_fiskur40 • updated 8 months ago by Kevin Blighe69k

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