Bowtie2 mapping did not finish, can I still use the .sam file?

Question

[jon.brate]

I mapped a set of paired reads using Bowtie2 but the job was cancelled before it finished. I don't need all the reads mapped for my purposes, so I wonder if I can still use the .sam file or if there are some steps performed at the very end of the mapping which affects the entire file? I am converting to .bam now and it seems to work at least.

Thanks

Answer 1

[WouterDeCoster]

I would think the file is corrupted, but if it converts to bam it seems to be valid... We obviously don't know what your "purposes" are.

[jon.brate]

Thanks. My interest was more general as I could always redo the mapping properly later. But in this case I'm going to use the mapping in Pilon to polish an assembly. I'm thinking to filter out only properly mapped pairs, and then I will assume nothing is wrong with the .bam file? (if nothing crashes along the way).

[GenoMax]

If your aim does not include others (including you) being able to reproduce this analysis then go ahead but otherwise you know what should be done :-)