Hello there, I am facing problem in interpreting Rockhopper output. I have bacterial RNAseq data which is single end and 50 bp read length. Reference database is available. There are duplicates for both the samples. I ran Rockhopper using following parameters checked "Reverse complement reads" and "Test for differential expression", but did not get any information regarding fold change. Also I got only Qvalues. I don't know how to find upregulated and downregulated genes from this output. The columns which I got in transcripts.txt are: Transcription_Start, Translation_Start, Translation_Stop, Transcription_Stop, Strand, Name, Synonym, Product, Expression_Control, Expression_Treated, qValue_Control vs Treated.
Any help would be much appreciated!! Thanks and regards!
•
written
by
Annie •
0 answers
No answers yet.
Log in to answer this question.
-
How to extract DEGs from GEO database
written by harrydo1892 •
-
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyna…
written by GenoMax
-
Downregulated Genes with GFOLD
written by jth
-
[R] Microarray analysis interpreting logFC after makeContrasts
written by mheiser1 •
Which version are you using?
The last time that I used Rockhopper (2017), I performed de novo transcriptome assembly an differential expression between 2 conditions. I then received 2 output files:
transcripts.txt contained the following columns:
Fold-change could be calculated from the 2 'Expression' columns. From the sequence column, I could ran blastx in order to infer the gene / protein relating to the sequence.