User: dk0319

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dk031920
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Posts by dk0319

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Pacific Bio Long Reads vs Illumina Short Reads
... Thanks for the insights. Has anyone had experiences with Bionano's genome imaging platform? If so what did you think, did it perform better then Pac Bio in detecting genomic structural variants? ...
written 22 days ago by dk031920
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Bionano Saphyr Structural Variant ID and Genome Assembly
... Has anyone encountered Bionano's Saphyr system yet for structural variant identification or genome assembly? If so, would you be open to sharing your experience? ...
genome assembly forum written 23 days ago by dk031920 • updated 21 days ago by zx875410.0k
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Forum: Pacific Bio Long Reads vs Illumina Short Reads
... Is anyone who has worked with both Illumina and Pac Bio generated NGS data open to discuss their experience with the two platforms? Did you notice any clear strengths/weakness? Especially as it pertains to genome assembly and structural variant discovery and/or RNA-seq analysis (both DE and splice d ...
next-gen forum alignment rna-seq written 24 days ago by dk031920 • updated 24 days ago by h.mon32k
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Answer: A: Large Count Discrepancy of Key Gene Between STAR and HISAT2
... After viewing the HISAT2 mapped reads with CLC software (cleaner compared to IGV), it appears that while there are a large number of reads that map to the IFI27 locus the majority, but not all, appear to be multi-mapping. When I repeated this with the STAR aligned reads, all reads mapped to IFI27 we ...
written 8 weeks ago by dk031920
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Comment: C: Large Count Discrepancy of Key Gene Between STAR and HISAT2
... They appear to be spanning exon junctions. Is there a method for assessing the individual reads, besides visually inspecting them? ...
written 9 weeks ago by dk031920
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Answer: A: Best way to get gene IDs for Salmon transcript output
... tximeta was able to compile all my quant.sf files and summarize to gene level ...
written 9 weeks ago by dk031920
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Comment: C: Using bedtools to identify genes that have overlapping chip-seq peaks
... This approach worked ...
written 9 weeks ago by dk031920
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Comment: C: Differential Expression Analysis with Salmon vs Genomic Aligners Like Star
... I ended up finding this, which offers a nice overview of the differences (https://www.biostars.org/p/400009/#400017 ). I am still curious to hear from people with experience working with both approaches to see if they ever encountered any issues. ...
written 9 weeks ago by dk031920 • updated 9 weeks ago by GenoMax96k
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Comment: C: Differential Expression Analysis with Salmon vs Genomic Aligners Like Star
... I used the internal quantmode along with ht-seq and feature counts ...
written 9 weeks ago by dk031920
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Differential Expression Analysis with Salmon vs Genomic Aligners Like Star
... Can anyone with experience using aligners like Salmon and STAR for RNA-seq comment on the strengths and weakness of one method over another. So far I have performed the alignments and quantification and noticed some pronounced differences in the generated counts and I was curious to hear the thought ...
alignment rna-seq written 9 weeks ago by dk031920 • updated 9 weeks ago by swbarnes29.6k

Latest awards to dk0319

Supporter 22 days ago, voted at least 25 times.
Scholar 8 weeks ago, created an answer that has been accepted. For A: Best way to get gene IDs for Salmon transcript output
Scholar 9 weeks ago, created an answer that has been accepted. For A: Best way to get gene IDs for Salmon transcript output

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