User: lshepard

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lshepard130
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Posts by lshepard

<prev • 36 results • page 1 of 4 • next >
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Answer: A: Creating genome alignment
... From the Gencode website: "Primary assembly: Nucleotide sequence of the GRCh38 (or GRCh37 if you want that) primary genome assembly (chromosomes and scaffolds) The sequence region names are the same as in the GTF/GFF3 files" The larger file contains all regions including assembly patches and ha ...
written 8 days ago by lshepard130
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Comment: C: Sample data for RNA STAR
... In addition to the above, just wanted to add the link to [GEO][1], since often times, publications mention it, so you may want to know that this is all related. [1]: https://www.ncbi.nlm.nih.gov/geo/ ...
written 23 days ago by lshepard130
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Comment: C: rpkm and raw count
... To add to the answer, you can compare sequencing data across the platforms as long as you know what is expected to potentially differ (although as the literature shows, there is good concordance between them). As to the cell lines, that depends upon what kind of questions you are trying to answer, b ...
written 6 weeks ago by lshepard130
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Comment: C: Merge FastQ Files
... Check [this][1] older thread out Be sure to check the replies within it. Also keep in mind you can merge the data after alignment as bam files with SAMtools. [1]: https://www.biostars.org/p/136025/ ...
written 9 weeks ago by lshepard130
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Answer: A: Display the results obtained from DAVID and g:profiler functional annotation to
... Hi, There are several ways to display that type of data. Two simple ways are: 1) Tables with GO terms and p-values (at the very least) 2) Bar plots of the top GO terms ordered by p-value More "prettier" ways include: 3) Append GO results to a heatmap, just as the example shown in the `ComplexH ...
written 9 weeks ago by lshepard130
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Comment: C: TOPHAT error in mapping left_kept_reads step during a mapping with fusion search
... Stick it to STAR then. No reason to go back to an older algorithm. ...
written 10 weeks ago by lshepard130
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Comment: C: TOPHAT error in mapping left_kept_reads step during a mapping with fusion search
... Not an answer, but an advice that you should use the newer aligners (e.g.: STAR, HISAT2). ...
written 10 weeks ago by lshepard130
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Comment: C: Differential expression of scRNA-seq after Seurat
... Thanks, I don't know why I was thinking it was better to keep the treatment groups as separate objects. It makes more sense now to merge them. I appreciate the input! ...
written 12 weeks ago by lshepard130
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Comment: C: Differential expression of scRNA-seq after Seurat
... I edited my reply because your answer made me think of the following: Since you need to keep everything within a single object, I could merge the objects (control vs treatment) and follow this up with FindMarkers correct? ...
written 12 weeks ago by lshepard130
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Differential expression of scRNA-seq after Seurat
... Hi, I am currently planning a scRNA-seq analysis and I would like to have some feedback from this community. As this is a Drop-seq run, I will be using the Seurat package to identify clusters of cells. However, the program does not perform differential expression among experimental conditions (only ...
rna-seq written 12 weeks ago by lshepard130 • updated 12 weeks ago by igor5.2k

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