Moderator: rpolicastro

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rpolicastro3.3k
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rpolicas
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Posts by rpolicastro

<prev • 433 results • page 1 of 44 • next >
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Answer: A: How RNAseq PCR amplication results in duplicates
... PCR amplification is common in both RNA-seq and scRNA-seq. The prevalence of duplicates in your sequenced library will be a function of library complexity (quantity of unique cDNAs before amplification) and sequencing depth. In general, the more complex the library, the deeper the library can be seq ...
written 8 hours ago by rpolicastro3.3k
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94
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Comment: C: Isoform detection of a gene using RNAseq
... By detect do you mean that you want to quantify reads associated with that transcript? If so, I would recommend using a program such as [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) to quantify transcripts. It builds an index using a fasta file of transcript sequences, so all you wou ...
written 10 hours ago by rpolicastro3.3k
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Comment: C: Bioinformatics questions sequence
... The first question is asking to write a regular expression that captures those sequences. Depending on what language you are writing this in there will be regex tutorials that you should go through. ...
written 16 hours ago by rpolicastro3.3k
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Comment: C: Help with for loop for sequence alignment using STAR
... You seem to be pointing to a salmon transcriptome index instead of a STAR genome index. ...
written 20 hours ago by rpolicastro3.3k
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Comment: C: Merging integrated datasets
... What strange results was the analysis giving? ...
written 21 hours ago by rpolicastro3.3k
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79
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Comment: C: Find sequences in a fast files present in another fasta file
... Do the sequences match exactly? Also, is there any match in the names? ...
written 1 day ago by rpolicastro3.3k
5
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669
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Answer: A: Single cell RNA-seq anlaysis
... Since this post has accumulated views, I'll add a few resources. I would consider the three most popular scRNA-seq frameworks to be [Seurat](https://satijalab.org/seurat/) (R), [Bioconductor](http://bioconductor.org/books/release/OSCA/) (R), and [Scanpy](https://scanpy.readthedocs.io/en/stable/) (P ...
written 1 day ago by rpolicastro3.3k
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Comment: C: Ratio of Log2FC
... This seems like a poor (fatal) experimental design at first glance. Since protein and injection amount are perfectly correlated, you won't be able to deconvolute the effect of protein from injection amount. What was the reasoning behind injecting different amounts? ...
written 1 day ago by rpolicastro3.3k
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Comment: C: How to interpret a single cell RNA-seq experiment with 10 times less cells but c
... Assuming Cell Ranger worked correctly, it likely means few cells were actually captured by the Chromium, and those few cells were over-sequenced by a factor of 100. Since it's likely an experimental error, you would need to consult with the people that loaded the cells. ...
written 4 days ago by rpolicastro3.3k
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Comment: C: Annotating two columns at the same time
... Can you include some example data, and an example of what you want the output to look like? ...
written 4 days ago by rpolicastro3.3k

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