Getting Intergenic regions, sRNAs and ORF from pyseer

[AbubakariAbdulwasid]

Hi Sir, please I have done GWAS using the three genetic variants (SNPs, unitigs and gene presence or absence) and want to locate Intergenic regions, sRNAs and ORF from my GWas. Is there a way to do that?

[mgalardini]

Hi, you can follow the tutorial for some hints into doing what you describe (i.e. annotating your hits): interpreting significant k-mers. You want to look into the annotate_hits_pyseer command, optionally including a few different --feature-type arguments

[AbubakariAbdulwasid]

when I use./annotate_hits_pyseer-runner.py significant_Unitigs2.txt Annotating_unitigs.txt EG1a_sRNA.txt --feature-type sRNA . I got usage: annotate_hits [-h] [--bwa BWA] [--tmp-prefix TMP_PREFIX] kmers references output annotate_hits: error: unrecognized arguments: --feature-type sRNA ,

[mgalardini]

Are you sure you have a recent version of pyseer? You can download the latest one, for which the option should be available. Another thing to mention is that you should check your GFF files to make sure the feature type you want to look for is in there; the feature type is the third column