User: Leon

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Leon0
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Posts by Leon

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Comment: C: Options Request for FeatureCounts
... I tried v1.6.2, but it still didn't work. ...
written 13 months ago by Leon0
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Comment: C: Options Request for FeatureCounts
... In featureCounts v1.6.0 (linux version), I found that `readExtension5` could not be set a negative value. The error message was 'Value for argumant --readExtension5 is out of range: 0 to 2147483647'. Could you fix it? Thanks! ...
written 13 months ago by Leon0
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Comment: C: Options Request for FeatureCounts
... If a read is extended before it is reduced, this can do what I wanna do. But according to your answers in the post ([Feature request for Rsubread::featureCounts: read length adjustment](https://support.bioconductor.org/p/59273/)), it seems to me that reduction happens prior to extension. So when usi ...
written 14 months ago by Leon0
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Options Request for FeatureCounts
... Hi, The options read2pos and readExtension3 are usefull for counting fixed fragments (https://support.bioconductor.org/p/59273/). Recently I considered one condition of counting reads based on their 5' most base, whose position was shifted. For example, the 5' most base is first shifted by a fixed n ...
featurecounts subread written 14 months ago by Leon0 • updated 14 months ago by Wei Shi3.2k
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Comment: C: Global expression shift using RUVSeq
... Thanks, Davide! The last thing I wanna confirm is "across samples" means comparing the same gene in different samples, and "across genes" means comparing different genes in one sample, right? ...
written 15 months ago by Leon0
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Global expression shift using RUVSeq
... Hi all, Does the Section 2.3 Differential expression analysis in RUVSeq vignette work in case of a global shift in exprssion? And can normalized counts obtained by normCounts(set1) be comparable directly between samples? Or should be transformed to CPM, TPM...? Thanks! ...
rnaseq normalization ruvseq differential expression written 15 months ago by Leon0 • updated 15 months ago by davide risso830

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