multiple hits

[nandy...@gmail.com]

Hello friends, 

I have a small doubt concerning gnumap software.

I want to try it to map reads but i have got a question about multiple hits.

If there are multiple positions for a read what is reported in the output file, all positions or just one of these ?

I mean when a read can be mapped in different positions, i wanted to know if the software will return just one random position or will it return one of the best mapping position for this read.

And is it possible with an option to have all the positions of that read ?

Advance thanks, 

[Nathan Clement]

If a single read aligns to multiple regions, the output will print to all the best locations.  ie:  if read q aligns to location G_1 and G_2 with score 0.98 and G_3 with score 0.95, GNUMAP will only print SAM records for G_1 and G_2.  There will be a column in the sam file (X0) that will tell how many total locations over the alignment threshold (-a argument) it aligns to.  

If you want to print all positions of the read, you can include the --print_all_sam flag and it will print out everything above the -a threshold.  

Let me know if this doesn't answer your questions.

Nathan

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