I recently tried to use bowtie2 and samtools to process some paired end data. I used bowtie2-build to index my reference genome, and used this index to align the paired end data. Once the alignment was over, i got the following on my STDOUT:
7659592 reads; of these: 7659592 (100.00%) were paired; of these: 136410 (1.78%) aligned concordantly 0 times 6927190 (90.44%) aligned concordantly exactly 1 time 595992 (7.78%) aligned concordantly >1 times 98.22% overall alignment rate
With this message, i assumed that the alignment is complete. I had used the -S option to obtain
sam output file. So i tried to use
index the output file, but every time i get
EOF not found error.
Please advise. Sameet