Hello, I am doing RNA-seq analysis, using the pipeline suggested here (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq). I utilized StringTie to map my reads, to assemble transcripts and to estimate transcript abundances. Reading throughout different posts I have decided to use DESeq2 package(count-based methods) for Differential expression analysis DESeq2 instead of Ballgown. Using the following commands:
python2.7 prepDE.py -i merged_list.txt
I obtain the following error:
Error: GTF file not found (/Ballgown/Adrenal_Cortex/)
My working directory is setting in "Prova" while my .gtf file is in "/Prova/Ballgown/Adrenal_Cortex/". The merged_list.txt file contains the ID Adrenal_Cortex in the first column and the path to .gtf file in the second column ("/Ballgown/Adrenal_Cortex/")
How can I solve my problem?
Thank you in advance for your suggestion!
0 answers
No answers yet.
Log in to answer this question.
-
Suggestion for Differential Expression analysis
written by Lorenzo •
-
DESeq2 Error: some variables in design formula are characters, converting to factors
written by Lorenzo •
-
count matrices for genes and transcripts for all samples
written by fatimarasool135
-
Stringtie: use htseq-count or prepDE.py to extract reads?
written by heyang •
-
Can I ignore these MSTRG genes in downstream analysis (pantherdb.org)?
written by Fawzi Yassine •
-
Error in prepDE.py in Tuxedo protocol after StringTie quantification
written by Mithil Gaikwad •
-
HISAT2, Stringtie,DEseq2 differential gene expression
written by sanchi.andrea •
-
Ballgown finds few DE genes compared to DESeq
written by corend
-
Stringtie to DESeq2
written by gozrom •
-
Using StringTie with DESeq2(StringTie geneID and corresponding Ensembl geneID)
written by Megan •
Try running the command from the directory where /Ballgown is located without specifying the input. Run just python2.7 prepDE.py
Thanks! Now it works. It was too easy. Thanks again!!!