I am using tophat2 for my rna seq data set. I mostly always use default options for tophat. I have some doubts when i see the accepted.hits.bam file
In the tophat manual it is written that
--max-insertion-length <int> The maximum insertion length. The default is 3
--max-deletion-length <int> The maximum deletion length. The default is 3
Now this means that in the CIGAR string in the alignment file i should never get a CIGAR string which has something like 4D or 5I because the default is 3 and these are max insertion and deletion length
But i still get something like this 39M5I4M1D28M or 71M4D5M
Am i missing something??
Secondly we have AS:i in tophat bam files. What is the best alignment score??? When i see bam files i see scores like AS:i:-29 and also like AS:i:-6 , AS:i:0
PS: isubmit tophat runs with my own genome created for 80 genes i am interested in. Can this cause the above problem??. I don't supply a gtf/gff file??
Hope to hear soon
Regards
Varun
In the tophat manual it is written that
--max-insertion-length <int> The maximum insertion length. The default is 3
--max-deletion-length <int> The maximum deletion length. The default is 3
Now this means that in the CIGAR string in the alignment file i should never get a CIGAR string which has something like 4D or 5I because the default is 3 and these are max insertion and deletion length
But i still get something like this 39M5I4M1D28M or 71M4D5M
Am i missing something??
Secondly we have AS:i in tophat bam files. What is the best alignment score??? When i see bam files i see scores like AS:i:-29 and also like AS:i:-6 , AS:i:0
PS: isubmit tophat runs with my own genome created for 80 genes i am interested in. Can this cause the above problem??. I don't supply a gtf/gff file??
Hope to hear soon
Regards
Varun