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Old 03-07-2014, 09:19 AM   #8
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
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Quote:
Originally Posted by Brian Bushnell View Post
Everything is there, and when you produce a sam file, you'll see that reads are mapped to all of the different input chromosomes.
So they are. Different mapping and slightly more -- in terms of raw matches -- than tophat. I'll have to do more work in order to see if the matches are accurate but so far it is encouraging.

Quote:
samtools idxstats BBMapped.bam | sort -n

* 0 0 174134
MT 16613 121832 3149
X 144288218 11619 559
Y 1637716 16 4
1 315321322 31627 2152
2 162569375 33762 1920
3 144787322 40457 3319
4 143465943 49722 2064
5 111506441 27714 1515
6 157765593 60316 2405
7 134764511 27906 2778
8 148491826 14523 1241
9 153670197 26155 1155
10 79102373 6924 601
11 87690581 13340 650
12 63588571 25561 1007
13 218635234 29541 1744
14 153851969 29737 2588
15 157681621 25974 2666
16 86898991 9360 334
17 69701581 23454 913
18 61220071 6550 332

Tophat accepted_hits.bam

Quote:
MT 16613 85810 0
X 144288218 11197 0
Y 1637716 12 0
1 315321322 35442 0
2 162569375 24092 0
3 144787322 46519 0
4 143465943 43747 0
5 111506441 22186 0
6 157765593 45857 0
7 134764511 18867 0
8 148491826 13938 0
9 153670197 27813 0
10 79102373 4661 0
11 87690581 12493 0
12 63588571 19511 0
13 218635234 33190 0
14 153851969 19774 0
15 157681621 11172 0
16 86898991 14862 0
17 69701581 19776 0
18 61220071 5159 0
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