User: sayuj.koyyappurath

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Posts by sayuj.koyyappurath

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Answer: A: Multiline Fasta To Single Line Fasta
... Hi Hope this works awk 'BEGIN{RS=">"}NR>1{sub("\n","\t"); gsub("\n",""); print RS$0}' file ...
written 5.7 years ago by sayuj.koyyappurath0
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Answer: A: Assess Cufflinks assembly
... Hi Please see the old posts in Biostar itself, may be you have seen it already! https://www.biostars.org/p/47224/ https://www.biostars.org/p/85039/   Best wishes   Sayuj ...
written 5.7 years ago by sayuj.koyyappurath0
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Comment: C: Problem with logFC values
... Ok sir, Thanks for the points. I will let you know, once i handle the data with limma.   Sayuj ...
written 5.7 years ago by sayuj.koyyappurath0
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Comment: C: Problem with logFC values
... Dear Dr.Devon I am working on the interaction b/w Orchid and Fusarium We have 2 types of Fusarium (Pathogenic (causes root rot of plant) and Non pathogenic) Plant type: Resistant and susceptible Pools used (combinations) Pool 1: Susceptible plant vs Pathogenic fungus  (we inoculated healthy pla ...
written 5.7 years ago by sayuj.koyyappurath0
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Comment: C: Problem with logFC values
... Dear Dr. Devon Thank you for the reply. Oh :( So i'm in wrong way. Thanks a lot for the guidance. Kindly let me know, how i can proceed with my datasets available. Thanks again! Sayuj ...
written 5.7 years ago by sayuj.koyyappurath0
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Comment: C: Problem with logFC values
... Thanks Russ I would also like to clarify my input file used for the logFC calculation, as mentioned below for Dr. Devon Ryan Please help me in this regard. I'm totally confused b/w raw counts and expected counts! Thanks a lot Sayuj ...
written 5.7 years ago by sayuj.koyyappurath0
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Comment: C: Problem with logFC values
... Thanks Devon for prompt reply The outsourced sequencing company provided me 2 types of files after the Abundance estimation using RSEM. (i have 8 pools/different combinations). So what they have done is they find the abundance estimation of each pools separately which gives different headers such ...
written 5.7 years ago by sayuj.koyyappurath0 • updated 5.6 years ago by RamRS28k
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Problem with logFC values
... Dear friends, I am basically a botanist and new to NGS. And i am sorry if any similar question was discussed before. Comparing Resistant and susceptible plant genotypes infected with Fusarium (Fungi) exp_study = DGEList(counts=rnaseqMatrix, group=conditions) exp_study = calcNormFactors(exp_study ...
R next-gen rna-seq logfc edger written 5.7 years ago by sayuj.koyyappurath0 • updated 5.6 years ago by RamRS28k

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