User: koaeb

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koaeb10
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Posts by koaeb

<prev • 5 results • page 1 of 1 • next >
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Comment: A: Differential gene expression analysis with RPKM
... I did find the limma method online. I was wondering if there are other methods available. Since I can't get the raw counts, I guess I have to report the limma method even though it is not ideal. Thank you! ...
written 6 days ago by koaeb10
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QC with RNA-SeQC output weird
... Hi, I have a set of RNA-seq data, I used STAR for mapping then used RNA-SeQC to check the quality. After STAR mapping I checked the Log.final.out file, there are 81% reads uniquely mapped. I then used RNA-SeQC to produce quality metrics. I used collapsed gtf as input. However in the metrics.tsv file ...
alignment quality control rna-seq star written 7 weeks ago by koaeb10
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Comment: C: Salmon with Sleuth
... Hi dsull, Thank you! ...
written 11 weeks ago by koaeb10
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Salmon with Sleuth
... Hi, I used "sleuth_prep(s2c, extra_bootstrap_summary = TRUE) " to create sleuth object, and I got a list contains obs_norm_filt, obs_norm and obs_raw, each of them also contains a tpm value. I searched lots of files online but none explained what's the difference among those data frames, especially ...
sleuth salmon rna-seq written 12 weeks ago by koaeb10 • updated 12 weeks ago by dsull1.6k
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Import Salmon output by tximport
... Hi, I'm new to this area, so my question may be very basic. I'm using tximport to estimate Salmon output to gene level counts, then perform DE analysis. Based on some online tutorial, I used `countsFromAbundance="lengthScaledTPM"`, but I'm not fully understand how exactly the counts were calculate ...
tximport R salmon rna-seq written 12 weeks ago by koaeb10 • updated 12 weeks ago by RamRS30k

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