User: mforde84

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Posts by mforde84

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Comment: C: Slight confusion about trimming paired end reads in RNAseq experiment
... Great, thanks for the clarification. ...
written 5 days ago by mforde841.0k
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Comment: C: Slight confusion about trimming paired end reads in RNAseq experiment
... Maybe I'm simply misunderstanding how library generation works. The inserted fragment should be size selected, my assumption was that the insert size was the expected size of the read? So if I have a 100bp read that means I'm sequencing the same 100bp fragment but from both directions. Or is it mor ...
written 5 days ago by mforde841.0k
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Slight confusion about trimming paired end reads in RNAseq experiment
... We have paired end RNAseq reads which were trimmed 15bp and 10bp at the beginning and end of each respective read. My question is if this is appropriate considering it seems that each read will now have an overhang compared to it's paired read. Wouldn't this make the paired reads mismatching simply ...
rnaseq written 5 days ago by mforde841.0k
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Comment: C: STAR index generation option --sjdbOverhang for paired-end ?
... Yes, that's correct. It's just read length - 1. ...
written 12 days ago by mforde841.0k
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Comment: C: Quantile normalizing prior to or after TPM scaling?
... Sorry for the delay. Yes, I ended up getting things to work. It's just an interesting question regarding how to use TPM/FPKM properly. I'm not sure if there are some benchmarking studies that look at this against the SEQC standards. If there aren't, it would probably make a good paper. I mean what's ...
written 12 days ago by mforde841.0k
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Comment: C: Quantile normalizing prior to or after TPM scaling?
... Unfortunately it's not TCGA data. It's a proprietary dataset. Hypothetically, say I wasn't able to get raw counts, how would you suggest doing between subject normalizations for TPM? TCGA does upper quartile normalization on it's FPKM and TPM data, that just didn't seem to do enough for my data set ...
written 14 days ago by mforde841.0k
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Comment: C: Quantile normalizing prior to or after TPM scaling?
... That's what I ended up doing. My main issue was with between sample normalizations of TPM, say if you don't have easy access to raw count data. Presumably the way I worded my post didn't get this across as well as it should have. ...
written 14 days ago by mforde841.0k
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Quantile normalizing prior to or after TPM scaling?
... Somewhat simple question, when is the most advantageous point in a RNAseq analysis to perform quantile normalization for future between sample comparisons? Would it be at the raw count level since the documentation on quantile normalization appears to require raw data? Is quantile normalization expe ...
rnaseq normalization written 15 days ago by mforde841.0k
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Comment: C: Retained intron transcripts
... I disagree. They are independent communities. Respectfully, it's none of your business where I post. Nor should you have any say in the moderation of my posts on another site. ...
written 28 days ago by mforde841.0k
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Retained intron transcripts
... Hi, We are seeing a retained intron transcript event for some RNAseq samples, and we want to assess at the sequence level which intron retention events are actually occuring. For example, we have support for DROSHA-203 which according to Ensembl is a retained intron transcript. However DROSHA-203 a ...
rnaseq written 28 days ago by mforde841.0k

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