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Old 01-04-2018, 05:12 AM   #11
niuyw
Junior Member
 
Location: china

Join Date: Feb 2016
Posts: 1
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Dear all and Brian Bushnell,

I'm using kmercountexact.sh to estimate the genome size of an insect. I tried 17 mer and 31 mer, but got different results. After reading all the discussions above, I still don't know how to do (perhaps due to my poor English...). Here are the codes and results:

1. k=17
Code:
kmercountexact.sh in=270B.0.fastq in2=270B.1.fastq k=17 khist=270.his out=270 peaks=270.peaks
and the 270.peaks:
HTML Code:
#k	17
#unique_kmers	502145545
#main_peak	47
#genome_size	574333111
#haploid_genome_size	574333111
#fold_coverage	24
#haploid_fold_coverage	24
#ploidy	1
#percent_repeat	86.388
#start	center	stop	max	volume
10	24	32	4706167	78178249	
32	47	118	5933924	195017237	
1097	1103	1256	2449	337060	
1256	1259	1300	1819	77545	
1300	1303	1368	1756	108489	
1368	1372	1374	1548	8989	
1374	1376	1391	1491	24859	
1391	1394	1421	1487	42110	
1421	1423	1435	1424	18973	
1435	1443	1498	1413	80666	
1498	1500	1517	1188	22777	
1517	1543	3853	1167	1077482
2. k=31
Code:
kmercountexact.sh in=270B.0.fastq in2=270B.1.fastq khist=270.31mer.his out=270.31mer peaks=270.31mer.peaks
and the 270.31mer.peaks:
HTML Code:
#k	31
#unique_kmers	877006010
#main_peak	41
#genome_size	846756437
#haploid_genome_size	423378218
#fold_coverage	20
#haploid_fold_coverage	41
#ploidy	2
#het_rate	0.01748
#percent_repeat	13.342
#start	center	stop	max	volume
8	20	32	12998950	229457745	
32	41	103	10571247	252163197	
702	705	748	4040	175332	
748	754	971	3523	588862	
971	973	1002	2005	59786	
1002	1007	1064	1870	108141	
1064	1065	1121	1635	89229	
1121	1123	1147	1515	37584	
1147	1154	1189	1392	56941	
1189	1198	1214	1327	32072	
1214	1216	1295	1267	95219	
1295	1304	3260	1131	896204
As you can see, the genome size are very different and ploidy are different. The insect is diploid, and it seems that the ploidy predicted is more accurate when using 31 mer.

I've also tried the Jellyfish way (http://koke.asrc.kanazawa-u.ac.jp/HO...enomesize.html) using 17 mer and got 707955101 bp. But I'm little doublt, is it a haploid size or total size?

Any suggestions would be appreciated. I'm totally stucked.
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