User: Haci

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Haci370
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Posts by Haci

<prev • 45 results • page 1 of 5 • next >
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... For RSEM check this [Biostars post][1] out. There is yet another link in that post where the creator of `DESeq2` answers a similar question. And for the log2(x+1) transformed ones, why can't you just exponentiate (and subtract 1)? [1]: https://www.biostars.org/p/320594/ ...
written 18 days ago by Haci370
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Answer: C: Subsetting Genes from Clusters
... `row.names(subset(marker.genes, cluster == 6))` ...
written 4 weeks ago by Haci370
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Answer: A: Differential gene expression
... Clustering does not have anything to do with the DE analysis. You can use normalized expression values but these need to be scaled first so each of your plus minus 100 genes would have the same effect/weight in clustering. Of course you can argue that if a gene is not differentially expressed across ...
written 5 weeks ago by Haci370
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Comment: C: Seurat integrated analysis - methods for cell-type specific responses
... Technically, they are not comparing DE results obtained with the `averaged expression` approach to those obtained with the`FindMarkers` approach. The former is performed for `CD4 Naive T cells` and `CD14 Monocytes` for `stim` vs `ctrl` comparison and the latter is used for `B cells`, again for `stim ...
written 6 weeks ago by Haci370
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Comment: C: Legends in FeaturePlot of Seurat Package
... A workaround would be using the `shape.by = NULL` parameter. You can give distinct shapes to your clusters. This would not be quite useful if you would have more than 3-4 clusters though. ...
written 6 weeks ago by Haci370
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Comment: C: MUC5AC is not present in deseq2 results
... I have no idea but I think it's worth being asked as a separate question. But did you confirm that it is really not in your annotation file? ...
written 9 weeks ago by Haci370
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Answer: C: MUC5AC is not present in deseq2 results
... Probably because it is not in the `gtf` file you used, hence my previous comment. ...
written 9 weeks ago by Haci370
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Comment: C: MUC5AC is not present in deseq2 results
... @ATpoint, do you think it is likely that a key gene in some malignancy is lost after independent filtering? @nazaninhoseinkhan, I would double check if your gene of interest is really present in your genome annotation file. There are major and minor versions, for example, `MUC2`, another mucine gen ...
written 9 weeks ago by Haci370
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Comment: C: cellranger count help
... As far as I can tell, the pipeline did not start either. One thing you can check is the extension, `cellranger count` would expect `fastq.gz`, just like your original files. If that would be the error, the software would have complained with an error though! ...
written 10 weeks ago by Haci370
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Comment: C: cellranger count help
... I don't think the `-F` option would be an issue, as it only effects the sequene/read name. `--split-files`, on the other hand, is critical, a typical 10x run has 2 or 3 `fastq` outputs, all of which are expected by `cellranger count` with the "right" ***filename*** (not read name) conventions. ...
written 10 weeks ago by Haci370

Latest awards to Haci

Scholar 10 weeks ago, created an answer that has been accepted. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Supporter 4 months ago, voted at least 25 times.
Scholar 6 months ago, created an answer that has been accepted. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Scholar 8 months ago, created an answer that has been accepted. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res

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