User: corend

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corend30
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Posts by corend

<prev • 27 results • page 1 of 3 • next >
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Comment: C: A very short gene with very high TPM
... What I am reading right now is that [TMM scaling is usable on expected read count and not on TPM values][1]. You think that I can use TMM on my TPM matrix? > TMM should be computed in terms of expected read counts. I tried TMM with edgeR: ***Input TPM Table:*** `o` o1 ...
written 5 months ago by corend30
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Comment: C: A very short gene with very high TPM
... My species does have an annotated transcriptome. But it is not comprehensive. I would to discover new transcript, and get the TPM expression for all of them. And on the one hand, use kallisto + tximport to find DE genes on my new transcriptome. And on the other hand have the TPM values for all genes ...
written 5 months ago by corend30
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Comment: C: A very short gene with very high TPM
... I did not asked myself those questions, I used fastQC on raw reads, seeing that quality is not optimal and that I had adapters. Then I used a cleaner ([UrQt][1]), and running fastQC on those cleaned reads I had no low quality bases, and no adapters anymore. I assumed that my data was ok for further ...
written 5 months ago by corend30
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Comment: C: A very short gene with very high TPM
... Just edited my post, thanks ...
written 5 months ago by corend30
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Comment: C: A very short gene with very high TPM
... I don't understand. 60% of my reads are not mapping to this gene. Only few of them are. But after TPM calculation it is 600k. Am I wrong? ...
written 5 months ago by corend30
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Comment: C: A very short gene with very high TPM
... > FPKM takes the gene-length into account, whereas TPM doesn't, What I read in your links doesn't say that? What I understand: TPM: Normalize per gene size, then library size. FPKM: Normalize library size, then gene size. I took my formula [here][1], but maybe I don't use it the right way. ...
written 5 months ago by corend30
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A very short gene with very high TPM
... I assembled my RNA-seq data using `cufflinks`. This computed FPKM for each gene assembled, and I converted it manually to TPM using: `[FPKM/sum(FPKM)]*1e6` I have a gene in all replicates that reaches 600k TPM, meaning that 60% of my transcripts are coming from this gene. I checked his length, 64nt ...
assembly rna-seq written 5 months ago by corend30 • updated 5 months ago by Friederike1.8k
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Comment: C: Why does cufflinks split this transcript?
... I guess you are right, if you want to post this as an answer I could validate it. Anyway, it means that on other transcripts, this problem might not be always present so it is ok for me. Thanks a lot :) ...
written 5 months ago by corend30
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Comment: C: Why does cufflinks split this transcript?
... It is : XXXXGA GTXXXXXXXXAG CGXXXXX Exon | intron | Exon ...
written 5 months ago by corend30
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Comment: C: Why does cufflinks split this transcript?
... I just filtered my bam and checked manually, they are still there. I also checked manually on igv, those junction reads are not secondary and are proper pair. ...
written 5 months ago by corend30

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