How to interpret sam file generated from BBMap?

Question

[O.rka]

I'm trying to figure out exactly which reads mapped to which sequence in my reference.

From the above, it looks like both: NS500647:152:HGNYTAFXX:1:11101:24950:3577 1:N:0:TTACCGAC and NS500647:152:HGNYTAFXX:1:11101:24950:3577 1:N:0:TTACCGAC were mapped to contig NODE_88_length_45187_cov_8.09805 but what about the ones without a reference in this field? Were these reads not mapped at all? If I wanted to get the reads that mapped to a specific reference, would I just ignore those?

Answer 1

[swbarnes2]

You need to learn to interpret sam flags.

http://www.samformat.info/sam-format-flag

But yes, those reads with no mapping position did not map to anything in your reference.

Answer 2

[h.mon]

Check Decoding SAM flags, flags 77 and 141 indicate unmapped reads. There are several posts on how to filter sam / bam files, if you search the forum you will find.

edit

hint: check samtools view to get reads mapped to just one chromosome.