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User: Thomas

gravatar for Thomas
Thomas • 20
Reputation:
20
Status:
New User
Location:
Columbia University
Last seen:
6 days, 17 hours ago
Joined:
1 week, 6 days ago
Email:
t*****@cumc.columbia.edu

Posts by Thomas

<prev • 8 results • page 1 of 1 • next >
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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 7 days ago by Thomas • 20
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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 8 days ago by Thomas • 20
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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 10 days ago by Thomas • 20
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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 10 days ago by Thomas • 20
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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 11 days ago by Thomas • 20
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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 12 days ago by Thomas • 20
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Comment: C: 6-bp deletions in RNA-seq data
... I have thought about that possibility, but 1) that would have to be an incredibly highly expressed gene, to make up such a huge proportion of total reads, and 2) the company that performed the original sequencing used hard trimming of the fastq files before alignment with TopHat. In their BAM files, ...
written 12 days ago by Thomas • 20
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6-bp deletions in RNA-seq data
... Hi Everyone, I am attempting to analyze RNA-seq data starting from fastq files. I have used HISAT2 to align the raw fastq files with default settings. No hard clipping or other modifications. The reference genome is mus musculus GRCm38. I then used samtools to convert SAM files to BAM files and nam ...
genome alignment sequence rna-seq written 12 days ago by Thomas • 20

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