User: mjavad2012

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mjavad20120
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Posts by mjavad2012

<prev • 7 results • page 1 of 1 • next >
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Comment: C: RNA-seq Differentially expressed genes analysis when there's no control treatmen
... Thank you for your response. So, just for my curiosity, what if we had 3 biological replicate for each 19 sample, is there any way to analyze this data and get DEGs? Secondly, what if I just wanna identify the unexpressed genes or unchanged genes (like PPR gene family) among my 19 species? Than ...
written 10 days ago by mjavad20120
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Comment: C: RNA-seq Differentially expressed genes analysis when there's no control treatmen
... Hi swbarnes2, Thank you for your quick response! 1. I can build DESeq object using DESeqDataSetFromMatrix() as following. > dds class: DESeqDataSet dim: 1165 19 metadata(1): version assays(1): counts rownames(1165): Contig4963g005220 Contig2758g005020 ... Contig3227g005030 Contig3720g006990 ro ...
written 11 days ago by mjavad20120
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RNA-seq Differentially expressed genes analysis when there's no control treatment and we just have multiple HKGs
... Hi All, I'm currently investigating DEG pattern among 19 sub-species of a legume plant and there is no treatment at all except 19 sub-species. Q#1. What is the best way to select the control genes (HKGs)? Some people (PLoS One. 2017; 12(9): e0185288) suggested "Selection of candidate reference gene ...
wgcna housekeeping genes (hkgs) deseq rna-seq written 11 days ago by mjavad20120 • updated 11 days ago by swbarnes26.7k
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Comment: C: How to extract exon sequences from annotated genome
... the exon ID must the exactly the same in both (genome.fa and file.gff) input files? thanks ...
written 4 months ago by mjavad20120
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Comment: A: How To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
... How can I get alignment.fasta using command line?? ...
written 12 months ago by mjavad20120
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Comment: C: stringtie Error: input file cannot be found
... yes, I did but i still have that error. what format supposed to be the output file after -l ? ...
written 2.5 years ago by mjavad20120
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stringtie Error: input file cannot be found
... Hello, I want to use StringTie to assemble transcripts for each sample, but when I run the stringtie, I have an error: Error: input file –l cannot be found! here is my command: stringtie -p 8 -G /annotation/Ghirsutum_458_v1.1.gene.gff3.gz -o NMHT-80-23.gtf –l NMHT-80-23 NMHT-80-23.bam ...
assembly sequence rna-seq alignment written 2.5 years ago by mjavad20120 • updated 12 months ago by spriyar10

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For stringtie Error: input file cannot be found

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