Dear All,


I tested how to set the "Number of mismatches allowed in the initial read 
mapping" as follows.



At first, I ran FASTQ Groomer on a dataset to get the number of total reads. 
The total number of the reads is 17510227.



Then I ran Tophat after set "Number of mismatches allowed in the initial read 
mapping" as 1, and then ran "flagstat" under "NGS: SAM Tools". Here is the 
statistic information of Thophat output:
18162942 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
18162942 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)



Next I ran Tophat after set "Number of mismatches allowed in the initial read 
mapping" as 0, and then ran "flagstat" under "NGS: SAM Tools". Here is the 
statistic information of Thophat output:
16100027 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
16100027 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)



Does it mean about 0.6 million reads are aligned for 2 times or more after I 
set "Number of mismatches allowed in the initial read mapping" as 1, however 
about 1.4 million reads can not be aligned because of more stringent setting? 
Which number should we choose?



Thanks.

Jianguang
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to