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Hi all, is it possible to count the reads mapping to a specific region of a gene from the accepted_hit.bam?
Thanks a lot!
Thanks a lot!
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I attempted to explain this here: http://seqanswers.com/forums/showthread.php?t=29621
Originally posted by pengchy View PostComment
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Hi Cole,
I tried to reproduce the results in the paper "Differential gene and transcript expression analaysis of RNA-seq experiments with TopHat and Cufflinks" but using TopHat2 and Cufflinks2 instead. According to the volcano plot generated by cummeRbund (built on R 3.2.2) there are no significant differences. However, there're a bunch of genes above -log10(p-value)=2 and distant from log2(fold change)=0 in it.
Please, I would really appreciate if you could give me some feedback on this.
- JordiComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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