Hi, I am running both gsanp and bwa with my chip-seq data against human genome. However when I used samtools to check the mapping rate, I have very different results from thses aligners.
samtools output when I used bwa to align my chip-seq data:
11051448 + 0 in total (QC-passed reads + QC-failed reads)
3415200 + 0 duplicates
3887939 + 0 mapped (35.18%:-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)
samtools output when I used gsnap to align my chip-seq data:
29486009 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
21878904 + 0 mapped (74.20%:-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)
I used the default prameter for both of the aligner. I have no idea why the mapping rate of bwa is much lower than the mapping rate of gsnap? And why the reads number is quite different? I will be very appreciate if anyone could help. Thank you!
samtools output when I used bwa to align my chip-seq data:
11051448 + 0 in total (QC-passed reads + QC-failed reads)
3415200 + 0 duplicates
3887939 + 0 mapped (35.18%:-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)
samtools output when I used gsnap to align my chip-seq data:
29486009 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
21878904 + 0 mapped (74.20%:-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)
I used the default prameter for both of the aligner. I have no idea why the mapping rate of bwa is much lower than the mapping rate of gsnap? And why the reads number is quite different? I will be very appreciate if anyone could help. Thank you!