User: csijst

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csijst0
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Posts by csijst

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Using STAR and DESeq2 for circRNA analysis
... Hi, I noticed a group that went for the ASH conference presented a poster, being able to conduct differentially expressed circRNAs using STAR and DESeq2 (https://ash.confex.com/ash/2018/webprogram/Paper113333.html). But from my understanding, rRNA depleted samples may not be able to present as accu ...
deseq2 star written 9 months ago by csijst0 • updated 9 months ago by Michael Love26k
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Comment: C: Does STAR recognise circRNA and map it for downstream application?
... Hi, Well, I do agree that STAR isn't part of the Bioconductor package. But I assumed that the 'star' tag was part of the said program. Thus the entry. The developer does not reply promptly, and was actually thinking of getting a faster response from the experienced users. I will understand if you ...
written 17 months ago by csijst0
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(Closed) Does STAR recognise circRNA and map it for downstream application?
... Hi,I understand that STAR aligner can recognise splicing junctions and are usually used for RNAseq data. But I'm also curious whether it will treat circular RNAs like a linear transcript and feature it in the sam file (output). Is this true? If not, then how exactly will it treat circRNA? Ty. ...
star circrna written 17 months ago by csijst0
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Comment: C: Is circular RNA read out as linear fragments during Rsubread-DESeq2
... This is good information. So what you mean is that Rsubread will use the annotations (from the gtf file) to gather information of a location, and count the number of reads that cover that area yes? In which, the reads could encompass either linear or circular RNA? Am I right to say that if the DESeq ...
written 18 months ago by csijst0
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Comment: C: Is circular RNA read out as linear fragments during Rsubread-DESeq2
... That I can understand. I believe the Rsubread is the one featuring the reads. But wanted to clarify at least before I lay the information on my colleagues. Thanks by the way. ...
written 18 months ago by csijst0
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Comment: C: Issues in generating workable rank file for GSEA
... Hi, I tried the command, dDif_res <- results(dLRT, contrast=c("treatment", "shRNA", "ctrl"), alpha=0.05, altHypothesis="greaterAbs", cooksCutoff=FALSE) head(dDif_res) But the output still shows NA for some of the genes. These genes do not have any baseMean as well. ...
written 18 months ago by csijst0
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Issues in generating workable rank file for GSEA
... Hi, I'm trying to generate a ranking file for my differential expressed genes that was generated via DESeq2. I saw some websites like Genome Spot that taught me how to use the p-values and log2foldchange to rank the genes. But in DESeq2 output, some of them appear as "NA". And this will reappear in ...
gseabase deseq2 gsea pre-ranked gsea written 18 months ago by csijst0 • updated 18 months ago by Michael Love26k
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Is circular RNA read out as linear fragments during Rsubread-DESeq2
... May I clarify a part of the DESeq2 package? Is it true that DESeq2 counts for linear (only) transcripts and excludes any possibility in circular RNA (circRNA)? In which, an increase/decrease in circRNA has no effect on the number of counts produced in the results/output? Or does DESeq2 not able to d ...
rsubread deseq2 circrna written 18 months ago by csijst0 • updated 18 months ago by Wei Shi3.2k
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About CIRI's output
... Hi, I tried finding information on CIRI's output details, but there is little to go around. Could someone help me with the interpretation? 1) So in the column heading, CIRI's output has the '#junction_reads', does this mean that there were X amount of junctions found within the start & end coo ...
splicesites splicing ciri written 18 months ago by csijst0
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Comment: C: Understanding data output of sailfish-cir
... Opps, sorry, I noticed my mistake. I have not sorted the information yet. So what I was looking at probably was not the correct information. ...
written 19 months ago by csijst0

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Popular Question 9 months ago, created a question with more than 1,000 views. For DESeq2 - DESeqDatasetFromMatrix

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