Dear all, After generating bunch of files with stringTie command line, I want to use DESeq2 for differential expression analysis. I understand that I have to create a matrix of read counts and the tool to use is prepDE.py,
prepDE.py -i list_gtf.txt
my output is
0 Treated_1 1 Treated_2 Traceback (most recent call last): File "/home/miniconda2/bin/prepDE.py", line 257, in <module> geneDict[geneIDs[i]][s]+=v[s] KeyError: 'Treated_2'
Here is my list
[@ws7910 Files.GTF]$ cat list_gtf.txt Treated_1 /home/RNAseq/HISAT/BAM/sorted/Files.GTF/Treated_1.gtf Treated_2 /home/RNAseq/HISAT/BAM/sorted/Files.GTF/Treated_2.gtf Treated_3 /home/RNAseq/HISAT/BAM/sorted/Files.GTF/Treated_3.gtf Untreated_1 /home/RNAseq/HISAT/BAM/sorted/Files.GTF/Untreated_1.gtf Untreated_2 /home/RNAseq/HISAT/BAM/sorted/Files.GTF/Untreated_2.gtf Untreated_3 /home/RNAseq/HISAT/BAM/sorted/Files.GTF/Untreated_3.gtf
The stringTie website says that for this purpose I have to use “files generated by StringTie (run with the -e parameter).” I used few command lines with stringtie, which one is it the one with that I was supposed to use the –e parameter? probably the error is due to that ..
my python version is Python 2.7.5
Thanks for support