User: Fawzi Yassine

gravatar for Fawzi Yassine
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Posts by Fawzi Yassine

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Comment: C: Can I ignore these MSTRG genes in downstream analysis (pantherdb.org)?
... ATpoint is a professional person so he wilil rightly think that I am complementing him in that reply, especially that I asked him another question. ...
written 11 weeks ago by Fawzi Yassine10
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Comment: C: Can I ignore these MSTRG genes in downstream analysis (pantherdb.org)?
... ATpoint I have always liked your replys But not this one. I have already done the assembly using stringtie (on AWS). Moreover I promised my would be employer to use stringtie I am only getting 167 proper gene id’s out of the 4077 significantly different genes. The rest have MSTRG tags in their id’s ...
written 11 weeks ago by Fawzi Yassine10
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Comment: C: Can I ignore these MSTRG genes in downstream analysis (pantherdb.org)?
... I did not understand this reply from the link you provided. "If you are interested only standard transcripts/genes (i.e Ensembl, all or targeted), it is okay to exclude MSTRG transcripts/genes for downstream analysis. But do not throw away those genes/transcripts. " ...
written 11 weeks ago by Fawzi Yassine10
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Can I ignore these MSTRG genes in downstream analysis (pantherdb.org)?
... Hi, I am using RNAseq analysis to find genes differentially expressed between 2 conditions. I am using StringTie for transcript assembly and quantification. I am using prepDE.py in order to use StringTie with DESeq2 as instructed on http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#des ...
stringtie deseq2 rna-seq written 11 weeks ago by Fawzi Yassine10 • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: Is lfcShrink only useful only for visualization?
... `lfcShrink_res_deseq2 = lfcShrink(dds=dds, coef = 2, res = res_deseq2, type = "apeglm")` gave 0.32 FC which is perfect! ...
written 12 weeks ago by Fawzi Yassine10
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Comment: C: Is lfcShrink only useful only for visualization?
... Hi Fred, So which one do you command that I report? The unshrunken LFC or the shrunken one? By the way that disease I am experimenting with end which I carry is called Friedreich’s Ataxia. ...
written 12 weeks ago by Fawzi Yassine10
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Comment: C: Is lfcShrink only useful only for visualization?
... The authors in (Lazaropoulos et al., 2015) said: ” Patients with FRDA have frataxin levels in peripheral tissues that range from 2% to 30% of control level” . So I guess researchers agree on the 0.3 FC number. Add I got this, but withot shrinking in deseq2 – which seems necessary in deseq2. Lazarop ...
written 3 months ago by Fawzi Yassine10
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Comment: A: Is lfcShrink only useful only for visualization?
... The authors in (Lazaropoulos et al., 2015) said: ” Patients with FRDA have frataxin levels in peripheral tissues that range from 2% to 30% of control level” (they used Western blot for measurements). So I guess researchers agree on the 0.3 FC number. Add I got this, but withot shrinking in deseq2 – ...
written 3 months ago by Fawzi Yassine10
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Comment: C: Is lfcShrink only useful only for visualization?
... Thank you for your reply. Actually, I am interested in (Fold Change) FC for a single gene FXN. For the biological condition I am testing, it has been shown (by microarray) that the FC for FXN is 0.3. In deseq2, the unshrunken FC is exactly 0.3 whereas the shrunken one is 0.45 That’s why I am relucta ...
written 3 months ago by Fawzi Yassine10
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Comment: C: lfcShrink function in DEseq2 is giving me an error
... Problem solved. Please, can you check this https://www.biostars.org/p/370268/? ...
written 3 months ago by Fawzi Yassine10

Latest awards to Fawzi Yassine

Popular Question 4 months ago, created a question with more than 1,000 views. For Affymetrix Microarray data
Scholar 4 months ago, created an answer that has been accepted. For A: ballgown has "." as Gene Names

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