User: shawn.w.foley

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shawn.w.foley180
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Posts by shawn.w.foley

<prev • 33 results • page 1 of 4 • next >
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Comment: C: Interpreting DEseq2 results
... That sounds like more of a biology question than a bioinformatics question. Based on the treatment would you expect global/general upregulation? Some treatments cause global gene silencing/upregulation so those results would be expected. Are you also applying a log2FoldChange cutoff? If you apply t ...
written 3 days ago by shawn.w.foley180
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Comment: C: Too low FPKM values from StringTie
... Try making a density plot of the log10(FPKM), that should show a more appropriate curve. And I'm not sure which output to recommend, I haven't used HiSat before, I tend to stick to STAR/HTSeq/DESeq2 or more recently Salmon/DESeq2. ...
written 4 days ago by shawn.w.foley180
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Comment: C: Too low FPKM values from StringTie
... Poor wording on my part. I think your data looks reasonable, 15-18k with >1FPKM is in the realm of what I normally see. I think the fact that you have ~75% of genes with <1 FPKM is because most of them just aren't expressed. I would set an expression threshold and then analyze everything above ...
written 5 days ago by shawn.w.foley180
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Answer: C: Too low FPKM values from StringTie
... How many genes have >0, >1, or >10 FPKM. What type of samples are these (cell line, tissue, etc). And how many genes are in your genome? It's not unreasonable to have an Ensembl annotation with >55,000 genes of which only ~8-15,000 genes are expressed. I'm wondering if annotated but une ...
written 5 days ago by shawn.w.foley180
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Comment: C: Unequally pooling libraries for RNAseq?
... I'd imagine that depends on well defined genomes. In this case it sounds like jingjin just has a mixture of various species together. Good advice for when I have a mixed sample in the future though! ...
written 10 days ago by shawn.w.foley180
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Answer: A: Unequally pooling libraries for RNAseq?
... From the experimental design I can't think of any issues with unequal pooling, most differential expression algorithms account for differences in sequencing depth. My concern would be the best way to remove the contaminating material. If you have a **VERY** well annotated fungal genome you can appl ...
written 11 days ago by shawn.w.foley180
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Answer: A: Get -400bp to +50bp sequence of gene from gff3 file
... You can extract out any arbitrary window using awk (or any coding language). Essentially you're asking to find the transcription start site (TSS) - 2000 and TSS + 50. You just need to be mindful of the strand a gene is coded on. GFF and BED files are formatted such that the "start" coordinate is alw ...
written 20 days ago by shawn.w.foley180
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Comment: C: How to identify translocation events within cell lines
... Are you suggesting a pool of primers, or are there panels for common/known breakpoints available? Thank you! ...
written 4 weeks ago by shawn.w.foley180
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Comment: C: How to identify translocation events within cell lines
... Thank you for the advice. In this case we're looking to verify reported translocations, so we do have *a priori* loci to test. Long reads likely won't be an option for our in-house sequencing core, but I'll look into it. ...
written 4 weeks ago by shawn.w.foley180
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Comment: C: How to identify translocation events within cell lines
... Nanopore would be a great idea, but we're restricted to Illumina. ...
written 4 weeks ago by shawn.w.foley180

Latest awards to shawn.w.foley

Popular Question 3 months ago, created a question with more than 1,000 views. For Analyzing RNA-seq without replicates
Scholar 3 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Popular Question 5 months ago, created a question with more than 1,000 views. For Analyzing RNA-seq without replicates
Scholar 13 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
Scholar 14 months ago, created an answer that has been accepted. For A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c

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