Moderator: igor

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igor11k
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Posts by igor

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Comment: C: how to calculate TMB from call stats file
... You can use GATK CallableLoci to get the number of covered bases. ...
written 1 day ago by igor11k
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Comment: C: Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
... The manual has human and mouse examples. However, it can use any gene sets as input. ...
written 4 days ago by igor11k
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Comment: C: Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
... Thanks for clarifying! If you are looking for an R-based tool, [clusterProfiler][1] is a good place to start. It does a few different types of analysis and includes many plotting options. [1]: http://yulab-smu.top/clusterProfiler-book/ ...
written 4 days ago by igor11k
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Answer: A: Do different cells transcribe different amounts of gene data?
... Different cells certainly have a different number of total transcripts and that should affect normalization. Unfortunately, there is no good way to assess the differences in total RNA. One solution is to use ERCC spike-ins, but this may introduce more problems than it solves and seems to be less pop ...
written 4 days ago by igor11k
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Comment: C: Best practices to perform a gene set enrichment analysis (GSEA) with E. coli?
... Based on the tools you listed, it sounds like you are looking for a web-based tool that does not require any coding? You can check a few additional options [here][1]. Most of those are going to only support specific species. If you are comfortable with some coding, there are many R-based tools that ...
written 4 days ago by igor11k
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Answer: A: "Bias" in NGS sequencing processing
... With NGS, you probably would not be measuring only 4 genes. It's not very common, but it's possible to perform targeted RNA-seq for specific genes of interest. In that case, you would also have housekeeping genes to use as controls. That would be analogous to more traditional methods like qPCR. ...
written 5 days ago by igor11k
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Comment: C: how to calculate TMB from call stats file
... You have to find out what kind of sequencing was done. Is it whole genome or exome? If exome, which panel was used? ...
written 5 days ago by igor11k
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Answer: A: GDC TCGA LUAD dataset iCluster.group parameter
... All the Pan-Cancer Atlas data (which is distinct from the project-specific TCGA datasets/publications) is easily accessible via [Xena][1] ([iCluster here][2]). [1]: https://xenabrowser.net/datapages/ [2]: https://xenabrowser.net/datapages/?dataset=TCGA_PanCan33_iCluster_k28_tumor&host=http ...
written 5 days ago by igor11k
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Comment: C: Timeline for hg39 human genome?
... Even if hg39 becomes available today, you probably should wait for the relevant external resources to catch up. Keep in mind that after almost 7 years, some databases and tools are still not updated to hg38 (not as many anymore, but definitely some). ...
written 6 days ago by igor11k
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Comment: C: Changing chromosome names in BAM files
... I am not sure how it uses chromosome names, but chr1_KI270892v1_alt is not the same thing as chr1. It would make as much sense to rename that as it would chr2 to chr1. While technically possible, it is not very meaningful. You probably should use samtools (or another tool) to filter for just the re ...
written 7 days ago by igor11k

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Good Question 17 days ago, asked a question that was upvoted at least 5 times. For Non-computational challenges in bioinformatics
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Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
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Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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