Error while mapping

[cirrusclouds09]

Working on a course project using public ENCODE paired-end ChIP-seq reads. Built an index with bowtie2-build, but running into this error: bowtie2-align exited with value 1. Tried both piped BAM and SAM outputs but no luck so far. Could it be input file format or something in the syntax? Thanks for any advice.

 

[Fantastic Mr. Fox]

I think it's possible to be a formatting issue considering how the reads are paired. Maybe you can double-check the input file paths and make sure they're unzipped and properly matched.

 

[Crazy_Dragonfruit80]

To add, double-check that your index prefix is correct and that your FASTQ files are properly formatted and accessible. Also, did you include the -x flag with just the index basename (not the full filename)? Sometimes a missing or mismatched file path causes this.