I am running a ChIP-Seq (pair-end) analysis for the first time and managed to find a good pipeline to follow. The pipeline is described in the following way
FASTQC - TRIMMOMATIC - FASTQC - BOWTIE2 - MACS2 callpeak - MACS2 bdgdiff - HOMER Peak annotation and motif discovery
My have managed to analyze my data with no problems up to the TRIMMOMATIC and the following FASTQC. However, when i run the BOWTIE2 (pair-end) with my data from the trimmomatic, the analysis is interrupted and gives me the folloring error message:
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/188.8.131.52 .
Execution resulted in the following messages:
Fatal error: Exit code 1 ()
As i am new to this, i don’t really know where the problem lies. I have tried to search for help on Biostars but couldn’t find anything conclusive for my analysis. Would anyone have a possible solution/advice on how to solve this problem?
Thank you very much in advance for all time and effort invested in my request