User: Thomas

gravatar for Thomas
Thomas30
Reputation:
30
Status:
New User
Location:
Columbia University
Last seen:
5 months, 1 week ago
Joined:
6 months, 1 week ago
Email:
t*****@cumc.columbia.edu

Posts by Thomas

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Picking the right genome annotation for RNA-seq
... Sorry, I should have been more explicit there. Yes, I have run the same data set with Ensembl and got around 90% unique gene assignments. I should also mention that the actual alignment rate was virtually identical between the Ensembl and UCSC HISAT2 alignments, ranging from 75% to 88%. So I think t ...
written 5 months ago by Thomas30
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Comment: C: Picking the right genome annotation for RNA-seq
... Yes, the Ensembl annotations have worked well, but I can't use them to view the read counts as histograms in the UCSC Genome Browser, due to the formatting differences. Unless there is a way to do this? :-) ...
written 5 months ago by Thomas30
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Picking the right genome annotation for RNA-seq
... Hi Everyone, I am aligning raw RNA-seq data from mouse samples for downstream analysis of differentially expressed genes. I would like to do this entirely based on UCSC data, to avoid mix-ups in the nomenclature and to be able to view bedGraph files in the UCSC Genome Browser later on. I used HISAT ...
gtf annotation rna-seq written 5 months ago by Thomas30
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Answer: A: Diverging read alignment and counts in TopHat vs. HISAT2
... Apparently, this problem is inherent to IGV. When we ran the same files that showed no reads on a different operating system, everything looked just fine. There are, of course, still differences between the Tophat and the HISAT2 alignments, but nothing is missing altogether. I will try to switch to ...
written 5 months ago by Thomas30
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Answer: A: 6-bp deletions in RNA-seq data
... Alright, I have followed Nancy's advice and extracted the read sequences that contained the 6-bp deletions. It turns out that the vast majority of them (ca. 80% in samples with lower number of 6-bp deletions, 99% in the sample with the highest number of 6-bp deletions) mapped to a specific region of ...
written 6 months ago by Thomas30
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Comment: C: 6-bp deletions in RNA-seq data
... Hi Nancy, This is an excellent starting point. I'll see if I can figure it out. Thank you! Thomas ...
written 6 months ago by Thomas30
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Comment: C: Diverging read alignment and counts in TopHat vs. HISAT2
... Right, exactly my problem! I can't tell if either of these is better than the other, if one is seriously flawed or if both of them are acceptable. What additional information would be helpful in determining this? ...
written 6 months ago by Thomas30
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Comment: C: Diverging read alignment and counts in TopHat vs. HISAT2
... Yes, it's GRCm38/Mm10. I should have mentioned that (just edited the original entry to include the information). So you think this is an acceptable level of quality for Mm10 alignments? ...
written 6 months ago by Thomas30
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Comment: C: 6-bp deletions in RNA-seq data
... Hm, I like that idea! Do you know how I can do this? ...
written 6 months ago by Thomas30
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Diverging read alignment and counts in TopHat vs. HISAT2
... Hi Everyone, We have commissioned RNA-seq and analysis by a company, which provided us with raw fastq files, BAM files, and a count matrix. They used hard clipping and Tophat for the alignment to GRCm38/Mm10. I have attempted to recreate their analysis with HISAT2 (same reference genome), using sim ...
genome alignment rna-seq written 6 months ago by Thomas30

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Scholar 5 months ago, created an answer that has been accepted. For A: 6-bp deletions in RNA-seq data
Scholar 6 months ago, created an answer that has been accepted. For A: 6-bp deletions in RNA-seq data

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