bowtie2 results with NGS data
Hello,
I made index from my reference file and run command to align my metagenomic data by bowtie2. command is
bowtie2 -x <index_referance> -1 <paired_end_read_path_1.fastq> -2 <paired_end_read_path_2.fastq> -s <outputname.sam>
and i got this result on screen without getting sam file in output folder.
16190304 reads; of these:
16190304 (100.00%) were paired; of these:
16189692 (100.00%) aligned concordantly 0 times
612 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
16189692 pairs aligned concordantly 0 times; of these:
59 (0.00%) aligned discordantly 1 time
----
16189633 pairs aligned 0 times concordantly or discordantly; of these:
32379266 mates make up the pairs; of these:
32379200 (100.00%) aligned 0 times
66 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
Can anybody tell me what are these results and what’s wrong with this?? please
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