Question: How to interpret sam file generated from BBMap?
0
gravatar for O.rka
9 weeks ago by
O.rka70
O.rka70 wrote:

enter image description here

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?

sequencing alignment • 148 views
ADD COMMENTlink modified 9 weeks ago by swbarnes24.6k • written 9 weeks ago by O.rka70
2
gravatar for swbarnes2
9 weeks ago by
swbarnes24.6k
United States
swbarnes24.6k wrote:

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.

ADD COMMENTlink written 9 weeks ago by swbarnes24.6k
2
gravatar for h.mon
9 weeks ago by
h.mon22k
Brazil
h.mon22k wrote:

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.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by h.mon22k
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