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