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:
# 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!