bismark - fasta alignment result?

[mbk0asis]

Hi.
I used 'bismark' to align bisulfite treated DNA sequences in the fasta format.
Bismark produced a .sam and a report file along with a overview pic.
When I opened the .sam file, it didn't contain any information about aligned sequence. So, I couldn't figure out which sequences were aligned. Please, somebody tell me how to get them.

[dpryan]

1. How did you open the SAM file.
2. What did the SAM file contain?

It's likely that you were just looking at the header and needed to scroll down.

[mbk0asis]

I opened the SAM files using 'less' command and tried to scrolled down to the end of the file. But the sam file contained only the header and nothing else.

Thanks, dpryan!

[dpryan]

Presumably you got an error at some point then. You'll have to find it and figure out why that happened.

[fkrueger]

If you could send the the onscreen text you see when running your FastA file via email I could try to help.