I am a bioinformatics novice and am trying to learn how to analyze my RNA-seq reads. I came across this program called SPARTA (Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis) which is designed for novices like myself. The program is Python based and functions via command prompt in Windows.
The first process in SPARTA's workflow appears to be quality control using Trimmomatic - and this is where my issues arise. When I run SPARTA, my sequencing read files are processed appropriately and it looks like Trimmomatic runs successfully. Then I am left with the following error message:
C:\Users\Ryan\Desktop\RNAseq_Data\2019-08-28_21\QC\trimmedGSF1906-Delta-hns-3_S66_R1_001.fastq.gz ILLUMINACLIP:\Users\Ryan\Desktop\SPARTA_Windows-master\QC_analysis\Trimmomatic-0.33/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences Quality encoding detected as phred33 Input Reads: 2574357 Surviving: 2553622 (99.19%) Dropped: 20735 (0.81%) TrimmomaticSE: Completed successfully Traceback (most recent call last): File "SPARTA.py", line 155, in <module> qc.trimmomatic(rawdatapath, subfolderpath, options) File "C:\Users\Ryan\Desktop\SPARTA_Windows-master\qc_analysis.py", line 103, in trimmomatic extension = file.split(".") IndexError: list index out of range
I'm currently very confused what the 'IndexError' is referencing and I'm unsure how to resolve this issue.
Any feedback would be greatly appreciated. Thank you!