Moderator: jared.andrews07

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jared.andrews076.2k
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Soon to be Bioinformatics Research Scientist at St. Jude Children's Research Hospital studying pediatric brain tumors. Ph.D. at Washington University in St. Louis performing comparative multi-omics studies on B and T cell lymphomas to identify their epigenetic underpinnings. I have a strong interest in the development of high-performance, flexible bioinformatic tools that can integrate multiple -omics datasets to yield interesting and plausible conclusions that can then be experimentally validated.

Avid Python user, fledgling R developer, hater of Perl. 

Posts by jared.andrews07

<prev • 709 results • page 2 of 71 • next >
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Comment: C: Copy column to another column in the same file
... Pipe it to a new file by tacking `> your_new_file.gff` on the end. ...
written 6 days ago by jared.andrews076.2k
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Answer: A: Gene ontology for differential genes (easy manual)?
... We're going to need more information. What do you want to do with the gene ontologies? Just enrichment? If so, there are multiple easy to use web servers and R packages that can run those analyses for you. Enrichr, g:profiler, clusterProfiler, topGO, and DAVID are all popular options that essentiall ...
written 6 days ago by jared.andrews076.2k
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Answer: A: Bioinformatics basics-Protein sequence and its interpretation
... You seem to be lacking a fair amount of general information here, so I'm going to do my best to provide some information and resources to help you learn. **1. What are protein structural motifs?** I'm assuming you mean structural motifs rather than sequences for DNA binding motifs here. A very sh ...
written 7 days ago by jared.andrews076.2k
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Comment: C: Free online seminars/journal club
... I've changed this to a News post rather than a Forum, as it's more an announcement than an open-ended discussion, just an FYI. ...
written 7 days ago by jared.andrews076.2k
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Comment: C: ChIP-seq analysis guidance for a beginner
... Depends. If they're FASTQ files, you'd want to do some QC to ensure the sequencing worked properly. Then you'd move on to the alignment and additional steps as I list above. If they're BAM files, you can also run them through FastQC, but would be able to skip the alignment step, assuming whoever did ...
written 7 days ago by jared.andrews076.2k
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Comment: C: ChIP-seq analysis guidance for a beginner
... Okay, replicates are good. Then your first step is to get the original data in FASTQ (or at least BAM) format. bigWig files have already been processed and are meant for visualization purposes. They are typically scaled, but are not directly comparable to one another in most cases. This is especia ...
written 7 days ago by jared.andrews076.2k
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Answer: A: ChIP-seq analysis guidance for a beginner
... How many replicates for each condition do you have? Generally, the ChIP-seq pipeline goes: - Sequencing QC (FastQC) - Alignment (many options here) - Peak calling & peak annotation (MACS2, ZINBA, lots of peak callers out there. chipSeeker is popular for peak annotations, though it takes ...
written 7 days ago by jared.andrews076.2k
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Answer: A: subsetting seurat object with multiple samples
... Generally, you'll want use different parameters for each sample. But even then, using a blanket threshold for all clusters in a sample may remove populations of biological interest. A recent question [here](https://www.biostars.org/p/446554/#446562) gets into that particular problem a bit. As an a ...
written 7 days ago by jared.andrews076.2k
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Answer: A: Does ncRNA belong in RNA-seq data?
... The FastQC overrepresented sequences are typically a result of adapters or other contaminants. See [here](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/9%20Overrepresented%20Sequences.html) for a full explanation. The solution is usually to trim the reads vi ...
written 8 days ago by jared.andrews076.2k
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Answer: A: 'No code' data manipulation tools for bioinformatics
... A list of common formats can be viewed [here](https://genome.ucsc.edu/FAQ/FAQformat.html) along with their specs. Particular emphasis on BED (or BED-like) formats, which are extremely common, in addition to VCF and GTF/GFF. Those (along with typical CSV/TSV) files are likely the most common formats ...
written 8 days ago by jared.andrews076.2k

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Scholar 8 days ago, created an answer that has been accepted. For A: How to make variant calling run faster?
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Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Visualization for ChIP-seq analysis
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