sk1350

Hello, Could it potentially be an issue with FIMO not being in my path? Other files are all correctly defined and are all in the same directory so I am...

Hello, So I checked my fa file and it seems to be in the wrong format. >ENSG00000015475;SE:chr22:18222254-18222848:18222942-18226569:-;down:**:chr22:18222647-18222847(-)** GTACTCGGGCAGGGGCAGCACGGAGGCTGTGCGCCAGAGGAGGAGGACTGAGGGGCAAGGGGGAGAGCTCTGGTTGGAAAGGCAGGGGAGATTCTCCAGGGCCTTGCCGGTGCCAGTGACAACTGGGGTTTTCCTGAGACGGGACTGCGAGGAATGGGGGCTCTCAGGCTTGAGAGGGCAAAAGTGGGTCTGGGATGCCG Compared to example fa file >ENSG00000015475;SE:chr22:18222254-18222848:18222942-18226569:-;down GTACTCGGGCAGGGGCAGCACGGAGGCTGTGCGCCAGAGGAGGAGGACTGAGGGGCAAGGGGGAGAGCTCTGGTTGGAAAGGCAGGGGAGATTCTCCAGGGCCTTGCCGGTGCCAGTGACAACTGGGGTTTTCCTGAGACGGGACTGCGAGGAATGGGGGCTCTCAGGCTTGAGAGGGCAAAAGTGGGTCTGGGATGCCG Which is probably why I...

I used the UCSC genome

The bed file (TEST_events_bedfile) looks like this chr22 45944292 45944492 ENSG00000077942;SE:chr22:45943084-45944493:45944624-45946372:+;up 0 + chr22 45944492 45944624 ENSG00000077942;SE:chr22:45943084-45944493:45944624-45946372:+;E 0 +

Do you have any suggestions as to why the following step (python MoSEA/mosea.py getfasta --bedfile TEST_events_bedfile --genome hg19.fa --output TEST_fafile) produces a file of the wrong format?