diff --git a/libsmallrna/libsmallrna/libsmallrna.pyx b/libsmallrna/libsmallrna/libsmallrna.pyx index 62a6caef6b0a13964d0d32f2f08f889e66dc8ff0..b0326e0357bf73c0a730743e0a2d8a68c8ff4c55 100755 --- a/libsmallrna/libsmallrna/libsmallrna.pyx +++ b/libsmallrna/libsmallrna/libsmallrna.pyx @@ -355,8 +355,13 @@ def count_sis(annot_infos, write_queue): # Eliminate most common non-siRNA target cases based on annotation name. # Also eliminate the reads with no signature # (the annot_name should be "no_signature") - if (annot_name in COMMON_NO_TARGET - or annot_name[:3] == "no_"): + # if (annot_name in COMMON_NO_TARGET + # or annot_name[:3] == "no_"): + # continue + # Actually, we do accept reads that do not start with G + # Provided they are not plain "no_signature" + # (that is: without other annotations) + if annot_name in COMMON_NO_TARGET: continue # annotations: set of tuples # (attrs["gene_biotype"], gtf.strand, gtf.start, gtf.end, attrs["gene_id"])