User: mark.ziemann
mark.ziemann • 1.2k
- Reputation:
- 1,250
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- Location:
- Australia/Mebourne/Geelong/Deakin
- Website:
- http://genomespot.blog...
- Twitter:
- @mdziemann
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- Google Scholar Page
- Last seen:
- 2 weeks ago
- Joined:
- 5 years, 1 month ago
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I'm a researcher and lecturer at Deakin University, Australia. I use Next Generation Sequencing to study epigenetics in a range of human diseases. Maintainer of the DEE2 RNA-seq database: http://dee2.io
Posts by mark.ziemann
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... It could be:
1. Difference in bisulfite conversion efficiency
2. Overall error rate differences in these seq runs - if you could obtain the phi-x from those runs you could check the error rates precisely
3. Something related to the alignment search space being twice as large for non-directional ...
written 4 weeks ago by
mark.ziemann • 1.2k
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... Are you able to use the SRA search and send the results to SRA run selector? Then you can collect a list of SRA runs (start with SRR.ERR.DRR) which you can pass to prefetch.
I have used SRAdb and SRAdbV2 in the past, but these packages are no longer maintained ...
written 5 weeks ago by
mark.ziemann • 1.2k
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... Duplicate question. You could try the suggested answer from a [previous post][1]
[1]: https://www.biostars.org/p/131329/#131449 ...
written 5 weeks ago by
mark.ziemann • 1.2k
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... Could you give the version of MACS2 you are using and specify which output file you are referring to. There should be a narrowPeak.bed file present among the results. If you also provide the command you used to perform the analysis it will help us troubleshoot it for you. ...
written 5 weeks ago by
mark.ziemann • 1.2k
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... Here is another paper that might be interesting where they discuss RNA-seq without replicates
[GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.][1]
[1]: https://www.ncbi.nlm.nih.gov/pubmed/22923299 ...
written 5 weeks ago by
mark.ziemann • 1.2k
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... Gene location information can be found in the GTF or GFF files on the [Ensembl FTP site][1]. You just need to make sure that the version of the GTF/GFF file you use is the same as the annotation of the gene list you received. Older versions of Ensembl can be found at the [archive][2].
Here is the f ...
written 7 weeks ago by
mark.ziemann • 1.2k
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... Is this an Ensembl transcript ID? If so, you can use [Ensembl BioMart][1] to obtain tables that relate transcript and gene IDs.
[1]: https://www.ensembl.org/biomart/martview ...
written 7 weeks ago by
mark.ziemann • 1.2k
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Comment:
C: /bin/bash/ command not found
... Apologies - I will edit ...
written 7 weeks ago by
mark.ziemann • 1.2k
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... 2 replicates is not very reliable. You will have a high rate of false positives and false negatives. That is just a fact of life.
Now with that out of the way, you could read the following:
- EdgeR paper, which talks about small number of replicates https://academic.oup.com/bioinformatics/article ...
written 7 weeks ago by
mark.ziemann • 1.2k
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... Yes, I think it is safe to convert Ensembl IDs to Entrez. Ensembl is more comprehensive especially WRT ncRNA genes. You will lose some of these, but those genes are also less likely to have annotations in the gene set databases you are using. The limitation of GSEA techniques is that many genes have ...
written 7 weeks ago by
mark.ziemann • 1.2k
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