I am a complete beginner so I am trying this out for practice. I am trying to align a read to a reference.
This is the read
head ali.fq
@GAII02_0001:1:115:1514:5351#0/2
G
+
C
This is the reference:
head test.fa
>TAIR45S
CCCTGCCCCT
I then use bwa to align the read:
$RSE = ali.fq
$REF=test.fa
bwa index $REF
bwa mem $REF $RSE > bwa.sam
My SAM file looks like
@SQ SN:TAIR45S LN:10
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem test.fa ali.fq
GAII02_0001:1:115:1514:5351#0 4 * 0 0 * * 0 0 G C AS:i:0 XS:i:0
I understand that the read consisting of only G got mapped but I don't know where in the output I can find the location of where G got mapped? Like in this example it got mapped to the 5th position.
Any help would be really appreciated.
I am only mapping one base as a demonstration. Sorry, bad example.
An example of one of my aligned reads looks like this.
Which position in the reference is my read mapped?
please, don't be lazy and read what fin swimmer wrote: