StringTie error

Question

[SHN]

Hello All,

I am running RNA-analysis using Hisat2/StringTie approach. and I want to use my output from the StringTie directly to the EdgeR.

The code that I used are as below:

hisat2 -p 8 --summary-file ./sampl1_summaryAlign.txt --dta -x ./grc38_tran/genome_tran -q -1 ./RwaData/read1.fastq.gz -2 ./RwaData/read2.fastq.gz | samtools sort -o ./sample1_sorted.bam

and then I use stringTie directly using -e option without merging.

stringTie -e -p -8 -G ./Homo_sapiens.GRCh38.113.gtf -o ./sample1.gtf ./sample1_sorted.bam 

First most of the gtf output has TPM 00, and Then when I try to make a list of samples and merge files using prepDE.py3 I get the error as below:

File "./home/prepFE.py3", line 282, in <module>
geneDict[geneIDs[I]][s[0]]+=v[s[0]]
KeyError: 'sample2

How should I solve this issue?

Is it better to run stringTie and merge all the gtf files and then re-un StringTie with option -e and then use the prepDE.py3?

Thanks for your help in advance,
SNGalaxy