BWA sai file is having different sizes for paired end

[himanshujain]

Hi all,
i am having a strange problem with BWA 0.5.9 windows version. When i processed paired end fq sequences to produce sai files they both are of different sizes (one is around 12Mb other one is 4Mb). and after that when i tried to create sam file using sampe for paired end it displays nothing.
So can anyone please help me regarding this? Is the sai file has to be like this or not? and what is the problem in generating sam files.
thanks a lot!

[vishnuamaram]

Hey himanshu,

First of all,
let me know how you are able to run alignment by BWA on windows. Thats k.


--> Up to my knowledge, i feel one of your paried end file say either Read1 or Read2 would have got corrupted or some of the reads in the file got deleted. That would be the possible reason.

-->I suggest you go back to your original file from where you got the data and compare the number of lines and sequences between original file and the file which gave only 4Mb size.

--> Hope this helps.

Regards,
Vishnu.