User: mjavad2012

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mjavad20120
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Posts by mjavad2012

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Comment: C: get original symbol for a non model organism
... Thank you for your response. So, what tool or command line you suggest to compare these with database sequences (refseq, uniprot) to find the matches? Thanks a lot. ...
written 10 weeks ago by mjavad20120
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get original symbol for a non model organism
... Hello Everyone, I have a new annotated genome and its annotation gff3 file and need to get original gene name or symbols. Is there any way to use chromosome:start:end information from annotation data and search in the other similar organisms (databases) and find the gene symbols or accession number ...
genome annotation gene symbol pathway analysis written 10 weeks ago by mjavad20120 • updated 10 weeks ago by JC10k
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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 9 months 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 9 months 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 9 months ago by mjavad20120 • updated 9 months ago by swbarnes28.1k
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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 13 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 22 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 3.3 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 3.3 years ago by mjavad20120 • updated 22 months ago by spriyar10

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Popular Question 3.3 years ago, created a question with more than 1,000 views. For stringtie Error: input file cannot be found

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