Hi! I mapped RNA-seq of Synechococcus sp PCC7002 and used this code:

bowtie -p 2 -C -S SynechococcusPCC7002 SRR308187.fastq > $SRR308187.sam

while it was mapping it gave me this information:

SRR308187

-reads processed: 26949795

-reads with at least one reported alignment: 13593071 (50.44%)

-reads that failed to align: 13356724 (49.56%)

Reported 13593071 alignments

No other file apart from SRR308187.sam were created. How can I get just the uniquely mapped reads?

I tried these codes:

samtools view -c -q 1 SRR308187.bam #(it gave me the number of reported alignments)

samtools view -bq 1 SRR308187.bam #(couldn't read it)

grep 'XS:' testfile.sam \
  | wc -l 
#(suppoused to give the number of alignments with more than 1 best align, but don't know if I have to just substract this number to the amount of reported alignments)

please help!