User: lshepard

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lshepard130
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Posts by lshepard

<prev • 38 results • page 1 of 4 • next >
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Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
... Perhaps the Biostars Slack group would be ideal for this? You could request to create a channel for the book itself and then for the lectures. It is worth a try (maybe for a test period of time). ...
written 6 weeks ago by lshepard130
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Comment: C: TCGA RNASeq Data
... Just a general advice on TCGA data: I would recommend to analyze the data from scratch (fastq files which you can acquire by using Picard Tools), rather then the provided BAM files. This is the only way that you can be sure that proper QC is being performed. ...
written 4 months ago by lshepard130
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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 5 months 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 5 months 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 months 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 7 months 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 7 months 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 7 months 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 7 months 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 7 months ago by lshepard130

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