User: Haci

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Haci370
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Posts by Haci

<prev • 46 results • page 1 of 5 • next >
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Comment: C: cellranger count help
... @genomax, technically, `R2` does not need to be the "largest" file. If longer read length is specified for `R1` during the sequencing run, exceeding the cell and transcript barcodes and into the transcript, `R1` can be equal to or larger than `R2`. ...
written 3 months ago by Haci370
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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 5 months ago by Haci370
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Answer: C: Subsetting Genes from Clusters
... `row.names(subset(marker.genes, cluster == 6))` ...
written 6 months 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 6 months 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 months 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 months 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 7 months 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 7 months 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 7 months 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 7 months ago by Haci370

Latest awards to Haci

Scholar 7 months ago, created an answer that has been accepted. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 7 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
Supporter 9 months ago, voted at least 25 times.
Scholar 11 months ago, created an answer that has been accepted. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Subsetting a set of genes of interest from DESeq2 res
Scholar 13 months ago, created an answer that has been accepted. For A: Subsetting a set of genes of interest from DESeq2 res
Teacher 13 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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