I am mapping some data using the new version of TopHat (2.0.4), that used the Bowtie2 to map the reads.
When I am looking at the log files from I dont understand somethings.
The tophat will prepare the reads and discard some, from the reads kept it will do in separate for the left and right side then mapping using bowtie2.
First it will do it for all the reads, and generate a report like this:
48857972 reads; of these:
48857972 (100.00%) were unpaired; of these:
7907873 (16.19%) aligned 0 times
33282945 (68.12%) aligned exactly 1 time
7667154 (15.69%) aligned >1 times
83.81% overall alignment rate
Then it will divide the reads into 4 segments of equal size and generate a
report to each segment similar to the one before.
bowtie.right_kept_reads_seg1:
14699739 reads; of these:
14699739 (100.00%) were unpaired; of these:
9578114 (65.16%) aligned 0 times
3519079 (23.94%) aligned exactly 1 time
1602546 (10.90%) aligned >1 times
34.84% overall alignment rate
bowtie.right_kept_reads_seg2:
14699739 reads; of these:
14699739 (100.00%) were unpaired; of these:
8957270 (60.93%) aligned 0 times
3879304 (26.39%) aligned exactly 1 time
1863165 (12.67%) aligned >1 times
39.07% overall alignment rate
bowtie.right_kept_reads_seg3:
14699739 reads; of these
14699739 (100.00%) were unpaired; of these:
8821548 (60.01%) aligned 0 times
3872784 (26.35%) aligned exactly 1 time
2005407 (13.64%) aligned >1 times
39.99% overall alignment rate
bowtie.right_kept_reads_seg4:
14699739 reads; of these:
14699739 (100.00%) were unpaired; of these:
9487826 (64.54%) aligned 0 times
3471682 (23.62%) aligned exactly 1 time
1740231 (11.84%) aligned >1 times
35.46% overall alignment rate
This step I didn't understand so well, because when summing up all the 4 segments the total size is bigger than the original, I think some of the reads
are repeated? How is this generated?
When I am looking at the log files from I dont understand somethings.
The tophat will prepare the reads and discard some, from the reads kept it will do in separate for the left and right side then mapping using bowtie2.
First it will do it for all the reads, and generate a report like this:
48857972 reads; of these:
48857972 (100.00%) were unpaired; of these:
7907873 (16.19%) aligned 0 times
33282945 (68.12%) aligned exactly 1 time
7667154 (15.69%) aligned >1 times
83.81% overall alignment rate
Then it will divide the reads into 4 segments of equal size and generate a
report to each segment similar to the one before.
bowtie.right_kept_reads_seg1:
14699739 reads; of these:
14699739 (100.00%) were unpaired; of these:
9578114 (65.16%) aligned 0 times
3519079 (23.94%) aligned exactly 1 time
1602546 (10.90%) aligned >1 times
34.84% overall alignment rate
bowtie.right_kept_reads_seg2:
14699739 reads; of these:
14699739 (100.00%) were unpaired; of these:
8957270 (60.93%) aligned 0 times
3879304 (26.39%) aligned exactly 1 time
1863165 (12.67%) aligned >1 times
39.07% overall alignment rate
bowtie.right_kept_reads_seg3:
14699739 reads; of these
14699739 (100.00%) were unpaired; of these:
8821548 (60.01%) aligned 0 times
3872784 (26.35%) aligned exactly 1 time
2005407 (13.64%) aligned >1 times
39.99% overall alignment rate
bowtie.right_kept_reads_seg4:
14699739 reads; of these:
14699739 (100.00%) were unpaired; of these:
9487826 (64.54%) aligned 0 times
3471682 (23.62%) aligned exactly 1 time
1740231 (11.84%) aligned >1 times
35.46% overall alignment rate
This step I didn't understand so well, because when summing up all the 4 segments the total size is bigger than the original, I think some of the reads
are repeated? How is this generated?