diff --git a/align.c b/align.c
index b4c00b1..25744e9 100644
--- a/align.c
+++ b/align.c
@@ -64,7 +64,7 @@ static int mm_check_zdrop(const uint8_t *qseq, const uint8_t *tseq, uint32_t n_c
 static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *tseq, const int8_t *mat, int8_t q, int8_t e, int q_intron)
 {
 	uint32_t k, l, toff = 0, qoff = 0;
-	int32_t s = 0, max = 0, min_intron_len;
+	int32_t s = 0, max = 0, min_intron_len, n_gtag = 0, n_ctac = 0;
 	min_intron_len = mm_min_intron_len(q, e, q_intron);
 	if (p == 0) return;
 	for (k = 0; k < p->n_cigar; ++k) {
@@ -96,10 +96,19 @@ static void mm_update_extra(mm_extra_t *p, const uint8_t *qseq, const uint8_t *t
 				p->n_ambi += n_ambi, p->n_diff += len - n_ambi;
 				s -= q + e * len;
 				if (s < 0) s = 0;
-			} else toff += len, p->blen += len;
+			} else { // intron
+				uint8_t b[4];
+				b[0] = tseq[toff], b[1] = tseq[toff+1];
+				b[2] = tseq[toff+len-2], b[3] = tseq[toff+len-1];
+				if (memcmp(b, "\2\3\0\2", 4) == 0) ++n_gtag;
+				else if (memcmp(b, "\1\3\0\1", 4) == 0) ++n_ctac;
+				toff += len, p->blen += len;
+			}
 		}
 	}
 	p->dp_max = max;
+	if (n_gtag > n_ctac) p->trans_strand = 1;
+	else if (n_gtag < n_ctac) p->trans_strand = 2;
 }
 
 static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) // TODO: this calls the libc realloc()
@@ -245,7 +254,7 @@ static void mm_fix_bad_ends(const mm_reg1_t *r, const mm128_t *a, int bw, int32_
 	}
 }
 
-static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r2, mm128_t *a, ksw_extz_t *ez)
+static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, uint8_t *qseq0[2], mm_reg1_t *r, mm_reg1_t *r2, mm128_t *a, ksw_extz_t *ez, int splice_flag)
 {
 	int32_t rid = a[r->as].x<<1>>33, rev = a[r->as].x>>63, as1, cnt1;
 	uint8_t *tseq, *qseq;
@@ -267,8 +276,9 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	mm_adjust_minier(mi, qseq0, &a[as1 + cnt1 - 1], &re, &qe);
 
 	if (opt->flag & MM_F_SPLICE) {
-		if (opt->flag & MM_F_SPLICE_FOR) extra_flag |= rev? KSW_EZ_SPLICE_REV : KSW_EZ_SPLICE_FOR;
-		if (opt->flag & MM_F_SPLICE_REV) extra_flag |= rev? KSW_EZ_SPLICE_FOR : KSW_EZ_SPLICE_REV;
+		if (splice_flag & MM_F_SPLICE_FOR) extra_flag |= rev? KSW_EZ_SPLICE_REV : KSW_EZ_SPLICE_FOR;
+		if (splice_flag & MM_F_SPLICE_REV) extra_flag |= rev? KSW_EZ_SPLICE_FOR : KSW_EZ_SPLICE_REV;
+		if (splice_flag & MM_F_SPLICE_BOTH) extra_flag |= KSW_EZ_SPLICE_FOR|KSW_EZ_SPLICE_REV;
 	}
 
 	// compute rs0 and qs0
@@ -368,6 +378,8 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
 	if (r->p) {
 		mm_idx_getseq(mi, rid, rs1, re1, tseq);
 		mm_update_extra(r->p, &qseq0[r->rev][qs1], tseq, mat, opt->q, opt->e, (opt->flag&MM_F_SPLICE)? opt->q2 : 0);
+		if (rev && r->p->trans_strand)
+			r->p->trans_strand ^= 3; // flip to the read strand
 	}
 
 	kfree(km, tseq);
@@ -450,7 +462,28 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
 	memset(&ez, 0, sizeof(ksw_extz_t));
 	for (i = 0; i < n_regs; ++i) {
 		mm_reg1_t r2;
-		mm_align1(km, opt, mi, qlen, qseq0, &regs[i], &r2, a, &ez);
+		if ((opt->flag&MM_F_SPLICE) && (opt->flag&MM_F_SPLICE_FOR) && (opt->flag&MM_F_SPLICE_REV)) {
+			mm_reg1_t s[2], s2[2];
+			int which, trans_strand;
+			s[0] = s[1] = regs[i];
+			mm_align1(km, opt, mi, qlen, qseq0, &s[0], &s2[0], a, &ez, MM_F_SPLICE_FOR);
+			mm_align1(km, opt, mi, qlen, qseq0, &s[1], &s2[1], a, &ez, MM_F_SPLICE_REV);
+			if (s[0].p->dp_score > s[1].p->dp_score) which = 0, trans_strand = 1;
+			else if (s[0].p->dp_score < s[1].p->dp_score) which = 1, trans_strand = 2;
+			else trans_strand = 3, which = (qlen + s[0].p->dp_score) & 1; // randomly choose a strand, effectively
+			if (which == 0) {
+				regs[i] = s[0], r2 = s2[0];
+				free(s[1].p);
+			} else {
+				regs[i] = s[1], r2 = s2[1];
+				free(s[0].p);
+			}
+			regs[i].p->trans_strand = trans_strand;
+		} else {
+			mm_align1(km, opt, mi, qlen, qseq0, &regs[i], &r2, a, &ez, opt->flag);
+			if ((opt->flag&MM_F_SPLICE) && !(opt->flag&MM_F_SPLICE_BOTH))
+				regs[i].p->trans_strand = opt->flag&MM_F_SPLICE_FOR? 1 : 2;
+		}
 		if (r2.cnt > 0) regs = mm_insert_reg(&r2, i, &n_regs, regs);
 		if (i > 0 && mm_align1_inv(km, opt, mi, qlen, qseq0, &regs[i-1], &regs[i], &r2, &ez)) {
 			regs = mm_insert_reg(&r2, i, &n_regs, regs);
diff --git a/format.c b/format.c
index 02cf3be..144005a 100644
--- a/format.c
+++ b/format.c
@@ -119,7 +119,11 @@ static inline void write_tags(kstring_t *s, const mm_reg1_t *r)
 	mm_sprintf_lite(s, "\ttp:A:%c\tcm:i:%d\ts1:i:%d", type, r->cnt, r->score);
 	if (r->parent == r->id) mm_sprintf_lite(s, "\ts2:i:%d", r->subsc);
 	if (r->split) mm_sprintf_lite(s, "\tzd:i:%d", r->split);
-	if (r->p) mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
+	if (r->p) {
+		mm_sprintf_lite(s, "\tNM:i:%d\tms:i:%d\tAS:i:%d\tnn:i:%d", r->p->n_diff, r->p->dp_max, r->p->dp_score, r->p->n_ambi);
+		if (r->p->trans_strand == 1 || r->p->trans_strand == 2)
+			mm_sprintf_lite(s, "\tts:A:%c", "?+-?"[r->p->trans_strand]);
+	}
 }
 
 void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const mm_reg1_t *r, void *km, int opt_flag, int intron_thres)
diff --git a/main.c b/main.c
index f387f2d..6a084fb 100644
--- a/main.c
+++ b/main.c
@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r296-dirty"
+#define MM_VERSION "2.0-r297-dirty"
 
 void liftrlimit()
 {
@@ -112,6 +112,7 @@ int main(int argc, char *argv[])
 			return 0;
 		} else if (c == 'u') {
 			if (*optarg == 'b') opt.flag |= MM_F_SPLICE_FOR|MM_F_SPLICE_REV;
+			else if (*optarg == 'B') opt.flag |= MM_F_SPLICE_BOTH;
 			else if (*optarg == 'f') opt.flag |= MM_F_SPLICE_FOR, opt.flag &= ~MM_F_SPLICE_REV;
 			else if (*optarg == 'r') opt.flag |= MM_F_SPLICE_REV, opt.flag &= ~MM_F_SPLICE_FOR;
 			else if (*optarg == 'n') opt.flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV);
@@ -153,7 +154,7 @@ int main(int argc, char *argv[])
 				opt.flag |= MM_F_SPLICE | MM_F_SPLICE_FOR | MM_F_SPLICE_REV;
 				opt.max_gap = 2000, opt.max_gap_ref = opt.bw = 200000;
 				opt.a = 1, opt.b = 2, opt.q = 2, opt.e = 1, opt.q2 = 32, opt.e2 = 0;
-				opt.noncan = 4;
+				opt.noncan = 5;
 				opt.zdrop = 200;
 			} else {
 				fprintf(stderr, "[E::%s] unknown preset '%s'\n", __func__, optarg);
diff --git a/map.c b/map.c
index f4ea657..f8654b2 100644
--- a/map.c
+++ b/map.c
@@ -38,6 +38,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
 
 void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
 {
+	if (opt->flag & MM_F_SPLICE_BOTH)
+		opt->flag &= ~(MM_F_SPLICE_FOR|MM_F_SPLICE_REV);
 	opt->max_occ = mm_idx_cal_max_occ(mi, opt->max_occ_frac);
 	opt->mid_occ = mm_idx_cal_max_occ(mi, opt->mid_occ_frac);
 	if (mm_verbose >= 3)
diff --git a/minimap.h b/minimap.h
index bce2448..c09b846 100644
--- a/minimap.h
+++ b/minimap.h
@@ -17,6 +17,7 @@
 #define MM_F_SPLICE      0x080
 #define MM_F_SPLICE_FOR  0x100
 #define MM_F_SPLICE_REV  0x200
+#define MM_F_SPLICE_BOTH 0x400
 
 #define MM_IDX_MAGIC   "MMI\2"
 
@@ -58,7 +59,8 @@ typedef struct {
 	uint32_t capacity;
 	int32_t dp_score, dp_max, dp_max2;
 	uint32_t blen;
-	uint32_t n_diff, n_ambi;
+	uint32_t n_diff;
+	uint32_t n_ambi:30, trans_strand:2;
 	uint32_t n_cigar;
 	uint32_t cigar[];
 } mm_extra_t;
diff --git a/mmpriv.h b/mmpriv.h
index 6f69467..83cfcf4 100644
--- a/mmpriv.h
+++ b/mmpriv.h
@@ -62,7 +62,8 @@ void mm_set_mapq(int n_regs, mm_reg1_t *regs, int min_chain_sc);
 
 static inline int32_t mm_min_intron_len(int32_t q, int32_t e, int32_t q_intron)
 {
-	return q_intron > q? (int)((float)(q_intron - q) / e + .999) : INT32_MAX;
+	int32_t x = q_intron > q? (int)((float)(q_intron - q) / e + .999) : INT32_MAX;
+	return x > 4? x : 4;
 }
 
 #endif