User: dk0319
dk0319 • 20
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- 7 months, 3 weeks ago
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Posts by dk0319
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... 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
dk0319 • 20
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... 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? ...
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... 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 ...
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... 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
dk0319 • 20
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... 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
dk0319 • 20
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... tximeta was able to compile all my quant.sf files and summarize to gene level ...
written 9 weeks ago by
dk0319 • 20
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... This approach worked ...
written 9 weeks ago by
dk0319 • 20
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... 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.
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... I used the internal quantmode along with ht-seq and feature counts ...
written 9 weeks ago by
dk0319 • 20
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6 follow
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... 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 ...
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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