User: Thomas
Thomas • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Columbia University
- Last seen:
- 8 months, 1 week ago
- Joined:
- 9 months, 1 week ago
- Email:
- t*****@cumc.columbia.edu
Posts by Thomas
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... 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 8 months ago by
Thomas • 30
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... 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 8 months ago by
Thomas • 30
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... 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 ...
written 8 months ago by
Thomas • 30
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... 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 8 months ago by
Thomas • 30
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... 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 9 months ago by
Thomas • 30
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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 9 months ago by
Thomas • 30
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... 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 9 months ago by
Thomas • 30
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... 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 9 months ago by
Thomas • 30
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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 9 months ago by
Thomas • 30
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... 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 ...
written 9 months ago by
Thomas • 30
Latest awards to Thomas
Scholar
8 months ago,
created an answer that has been accepted.
For A: 6-bp deletions in RNA-seq data
Scholar
9 months ago,
created an answer that has been accepted.
For A: 6-bp deletions in RNA-seq data
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