Hey guys,
I have paired end reads on RNASeq data and I wanted to test run Tophat2 to map these reads for a given sample using 5 different -r values(that is the mean inner distance between paired ends) just to see how it would affect the alignment.
I'm not exactly sure what I should look at once the alignment is over to figure out the so called 'alignment results'.
Tophat2 gives out a log folder along with the accepted_hits.bam, junction.bed files etc. in which I looked at two files namely:
bowtie.left_kept_reads.fixmap.log
bowtie.right_kept_reads.fixmap.log
These give summaries on the alignment from each end such as:
22630038 reads; of these:
22630038 (100.00%) were unpaired; of these:
2447457 (10.82%) aligned 0 times
15049769 (66.50%) aligned exactly 1 time
5132812 (22.68%) aligned >1 times
89.18% overall alignment rate
Now I notice there are also log files namely:
bowtie.right_kept_reads_seg1.fixmap.log
bowtie.right_kept_reads_seg2.fixmap.log
bowtie.right_kept_reads_seg3.fixmap.log
bowtie.right_kept_reads_seg4.fixmap.log
(And the same 4 for the left kept reads)
I don't understand what these files are or how they are different from the file I mentioned earlier (fixmap.log file)
I'm not sure if I'm looking at the correct log file, and if the fixmap.log file is indeed the right one to look at, I noticed that the alignment percentage is the SAME (i.e. 89%) for ALL -r options (I tried -50, -16, -33, 0, 50) using the same std deviation value. I just cannot understand why!!! - Does this mean that the -r option doesn't make a big difference in the alignment???
Hope to hear back from you guys soon. Thanks a lot.
I have paired end reads on RNASeq data and I wanted to test run Tophat2 to map these reads for a given sample using 5 different -r values(that is the mean inner distance between paired ends) just to see how it would affect the alignment.
I'm not exactly sure what I should look at once the alignment is over to figure out the so called 'alignment results'.
Tophat2 gives out a log folder along with the accepted_hits.bam, junction.bed files etc. in which I looked at two files namely:
bowtie.left_kept_reads.fixmap.log
bowtie.right_kept_reads.fixmap.log
These give summaries on the alignment from each end such as:
22630038 reads; of these:
22630038 (100.00%) were unpaired; of these:
2447457 (10.82%) aligned 0 times
15049769 (66.50%) aligned exactly 1 time
5132812 (22.68%) aligned >1 times
89.18% overall alignment rate
Now I notice there are also log files namely:
bowtie.right_kept_reads_seg1.fixmap.log
bowtie.right_kept_reads_seg2.fixmap.log
bowtie.right_kept_reads_seg3.fixmap.log
bowtie.right_kept_reads_seg4.fixmap.log
(And the same 4 for the left kept reads)
I don't understand what these files are or how they are different from the file I mentioned earlier (fixmap.log file)
I'm not sure if I'm looking at the correct log file, and if the fixmap.log file is indeed the right one to look at, I noticed that the alignment percentage is the SAME (i.e. 89%) for ALL -r options (I tried -50, -16, -33, 0, 50) using the same std deviation value. I just cannot understand why!!! - Does this mean that the -r option doesn't make a big difference in the alignment???
Hope to hear back from you guys soon. Thanks a lot.
Comment