Hi,

I have paired end reads Illumina 1.9 encoding. I am trying to figure out a way to see the reads that are multimapped, from the sam file.

To test this I created a database (an index file) using bowtie2 from a fasta file that contains a whole genome for Bacteroides vulgatus ATCC 8482 species but I copied the same genome twice in the same fasta file before creating the index file. I did this intentionally to check for duplicate reads. I deally any read that will be mapped to this genome should be mapped twice since I have the exact same sequence in my database twice.
To create the index file I issued the following command:

    $BT2_HOME/bowtie2-build /home/mstambou/represantative_gut_species/duplidate_genomes.fna duplicate_genomes_indices/duplicate_genomes_db

and then to map the reads to the created database I issued the following command:

    $BT2_HOME/bowtie2 --threads 24 -x duplicate_genomes_indices/duplicate_genomes_db -1 /home/team/hutternhower14/info/trimmed_1/gut_DNA/SRR769540-trimmed.1.fq -2 /home/team/hutternhower14/info/trimmed_1/gut_DNA/SRR769540-trimmed.2.fq -S X317802115/mapping_duplicate/SRR769540_duplicate.sam

the output of my last command is the following:

    4280027 reads; of these:
      4280027 (100.00%) were paired; of these:
        4144369 (96.83%) aligned concordantly 0 times
        2 (0.00%) aligned concordantly exactly 1 time
        135656 (3.17%) aligned concordantly >1 times
        ----
        4144369 pairs aligned concordantly 0 times; of these:
          0 (0.00%) aligned discordantly 1 time
        ----
        4144369 pairs aligned 0 times concordantly or discordantly; of these:
          8288738 mates make up the pairs; of these:
            8251346 (99.55%) aligned 0 times
            16 (0.00%) aligned exactly 1 time
            37376 (0.45%) aligned >1 times
    3.61% overall alignment rate

This output is in agreement of what I expect to see, it's saying non of the reads (other than 2 for some reason) are mapped 1 time, and most of them (the ones that are mapped) are mapped more than 1 time. But when I later check the sam output file I only see each read ID once (i.e. each read only has one row in the sam output).
I thought I should see more than one occurrence of the read IDs that are multi mapped. I really don't understand the reason behind this. I am pasting a sample of my sam file just for reference (the rows are sorted alphabetically using the read IDs).

    @HD	VN:1.0	SO:unsorted
    @SQ	SN:CP000139.1	LN:5163189
     @SQ	SN:copy_2	LN:5163189
    @PG	ID:bowtie2	PN:bowtie2	VN:2.3.4.2	CL:"/home/mstambou/bowtie2/bowtie2-2.3.4.2/bowtie2-align-s --wrapper basic-0 --threads 24 -x duplicate_genomes_indices/duplicate_genomes_db -S X317802115/mapping_duplicate/SRR769540_duplicate.sam -1 /home/team/hutternhower14/info/trimmed_1/gut_DNA/SRR769540-trimmed.1.fq -2 /home/team/hutternhower14/info/trimmed_1/gut_DNA/SRR769540-trimmed.2.fq"
    SRR769540.1001033.1	89	copy_2	4066024	0	99M	=	4066024	0	GTATCACATTTATCACAGTAGGTCTGATGGCAATCGCATTTATGTGTTTCTCTGGTTTGAACATCTAAAAAGAAAGGAATAAGACAATGGATATGAGCA		
    SRR769540.1001033.2	165	copy_2	4066024	0	*	=	4066024	0	TGGCTTACTCTGACGTGCCTGCTCCGTTGAAGGGCTTGGGTATCACATTTATCACAGTAGGTCTGATGGCAATCGCATTTATGTGTTTCTCTGGTTTGAAC	B	
    SRR769540.1001041.1	99	copy_2	2179441	1	101M	=	2179495	155	TATCTCCATTAGCGAAAACAGGCGCATGATACATCTTTCCACAGGCCTTTGCATAAGCAATCTGAGTGGACTCTTCATCCAAAGCCTCCCAGCGAGCTTTT	:??BDB:2C<<A;EEEAECD??+1???;B4?B>B*BA	
    SRR769540.1001041.2	147	copy_2	2179495	1	101M	=	2179441	-155	AAGCAATCTGAGTGGACTCTTCATCCAAAGCCTCCCAGCGAGCTTTTACACGCATCTCCTGCACTGCTTCATAAGCTAACTTCTGTACGTGAAAGCGATCG	CCAC>A>>>A>C	
    SRR769540.1001043.1	101	copy_2	2179939	0	*	=	2179939	0	TAGCGGTTCTGAAGACCAGCTAAGTTCTGGAACACGCATGACATGGACAGATTTCTGGAACGAATGACCGAAAT	7>=AA=7<=B<4,<<7+233+?>=2?=	
    SRR769540.1001043.2	153	copy_2	2179939	1	101M	=	2179939	0	CCAATAAATCCCCGTCAACTCCAGATAAAACACCTAAGAGCTTGCAACTGATCGGATAGCTATCAATATAGTTCTTTTAAAAAAGACGCAAAATCTTGCGT		
    SRR769540.1001566.1	89	copy_2	4992489	0	7M1I5M1D88M	=	4992489	0	GATTTCTCTTTCTCTTTTTAGTTTTCTTAGTCAAAATATGACTATGAAAAGCGTGCTTTCTTTTGATTTTACCTGTTCCGGTAAGGGTAAACCTTTTTTTA	DCDCDCDDCC?CDDDDCDDCDDDDCCDDDDDDEECEC	
    SRR769540.1001566.2	165	copy_2	4992489	0	*	=	4992489	0	GTTCCTTAACCTGGCTTAGATTTGTTGTATCAACAGTTGTAGAGTAGCACAGATTTCTCTTTCTCTTTTTAGTTTTCTTAGTCAAAATATGACTATGAAAA		
    SRR769540.1001567.1	89	copy_2	4992500	0	101M	=	4992500	0	CTCTTCTTAGTTTTCTTAGTCAAAATGTGACTGTGAAAAGCGTGCTTTCTTTTGATTTTACCTGTTCCGGTAAGGGTAAACCTTTTTTTAGAACCGGAGTT	A?>CCCCACDCCCCACDDDDCDBCC:CAC	
    SRR769540.1001567.2	165	copy_2	4992500	0	*	=	4992500	0	TTTACGCTTTTGATTACTTCATTGCTAAGAGTTCCTTAACCTGGCTTACATTTGTTGTATCAACAGTTGTAGAGTAGCACAGATTTCTTTTTCTCTTCTTA		
    SRR769540.1001573.1	69	CP000139.1	4992236	0	*	=	4992236	0	CGCTGCGTGAAGTAGCGGCGCTAACATTCAAAAAAAGTAAAACTATGCCAAGATCAGTAAATCATGTTGCTTCAAAAGCAAGAAGAAAGAAAATTTTGAAA		
    SRR769540.1001573.2	137	CP000139.1	4992236	0	84M1D17M	=	4992236	0	AAGTAACCTCTGGTTAATTTCAAAATTTTCTTTCTTCTTGCTTTTGAAGCAACATGATTTACTGATCTTGGCATAGTTTTACTTTTTTTGAATGTTAGCGC	C	

As you can see each read ID is only present once. Am I issuing the wrong command in bowtie? that maybe it's only showing me the primary hits? Im very new to this field and am sorry in advance for the novice question.

thanks.
The default is to show only the primary hits (it's usually what you want). If you want it to report the secondary alignments then use `-k`, though you may need to filter groups of reads afterward and you're not guaranteed that the primary hit will be the best possible hit that could be reported (though in practice it's highly likely to be).