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Aligning multiple fastq files in Bowtie2

I am trying to align multiple fastq file in bowtie2. I am using the following command line code

 ./bowtie2 -t -x bss  -1 C52.1.fastq,C55.1.fastq -2 C52.2.fastq,C55.2.fastq -S C5255.sam

But its seems that only the first file is getting aligned. the out put is showing results like this

Time loading reference: 00:00:07
Time loading forward index: 00:00:18
Time loading mirror index: 00:00:11
Multiseed full-index search: 00:00:38
16906 reads; of these:
  16906 (100.00%) were paired; of these:
    5902 (34.91%) aligned concordantly 0 times
    8736 (51.67%) aligned concordantly exactly 1 time
    2268 (13.42%) aligned concordantly >1 times
    ----
    5902 pairs aligned concordantly 0 times; of these:
      1170 (19.82%) aligned discordantly 1 time
    ----
    4732 pairs aligned 0 times concordantly or discordantly; of these:
      9464 mates make up the pairs; of these:
        5117 (54.07%) aligned 0 times
        2813 (29.72%) aligned exactly 1 time
        1534 (16.21%) aligned >1 times
84.87% overall alignment rate
Time searching: 00:01:14
Overall time: 00:01:15

When i run it using only one pair of read, the output is similar

$ ./bowtie2 -t -x bss -1 C52.1.fastq -2 C52.2.fastq -S C52.sam
Time loading reference: 00:00:08
Time loading forward index: 00:00:18
Time loading mirror index: 00:00:14
Multiseed full-index search: 00:00:38
16906 reads; of these:
  16906 (100.00%) were paired; of these:
    5902 (34.91%) aligned concordantly 0 times
    8736 (51.67%) aligned concordantly exactly 1 time
    2268 (13.42%) aligned concordantly >1 times
    ----
    5902 pairs aligned concordantly 0 times; of these:
      1170 (19.82%) aligned discordantly 1 time
    ----
    4732 pairs aligned 0 times concordantly or discordantly; of these:
      9464 mates make up the pairs; of these:
        5117 (54.07%) aligned 0 times
        2813 (29.72%) aligned exactly 1 time
        1534 (16.21%) aligned >1 times
84.87% overall alignment rate
Time searching: 00:01:18

Why is it so. I am new to bioinformatics. Any help is appreciated.

Thanks

bowtie2 alignment fastq
• 5,048 views • link
written by vineethmails • vineethmails

What happens if you call bowtie on the other set of fastq files ?

./bowtie2 -t -x bss -1 C55.1.fastq -2 C55.2.fastq -S C55.sam
• 0 views • link
written by Carlo Yague Carlo Yague 
$ ./bowtie2 -t -x bss -1 C55.1.fastq  -2 C55.2.fastq -S C55.sam
Time loading reference: 00:00:07
Time loading forward index: 00:00:18
Time loading mirror index: 00:00:13
Multiseed full-index search: 00:01:10
28255 reads; of these:
  28255 (100.00%) were paired; of these:
    7675 (27.16%) aligned concordantly 0 times
    15831 (56.03%) aligned concordantly exactly 1 time
    4749 (16.81%) aligned concordantly >1 times
    ----
    7675 pairs aligned concordantly 0 times; of these:
      1384 (18.03%) aligned discordantly 1 time
    ----
    6291 pairs aligned 0 times concordantly or discordantly; of these:
      12582 mates make up the pairs; of these:
        7543 (59.95%) aligned 0 times
        3169 (25.19%) aligned exactly 1 time
        1870 (14.86%) aligned >1 times
86.65% overall alignment rate
Time searching: 00:01:48
Overall time: 00:01:48

It gives this result

• 0 views • link
written by vineethmails • vineethmails

Whats your bowtie2 version? Can you try updating it? If the problem persists (this is not an answer to your question) you can concatenate the fastq files and run Bowtie2.

• 0 views • link
written by Satyajeet Khare Satyajeet Khare 
 $ ./bowtie2 -version
Bowtie 2 version 2.3.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
• 0 views • link
written by vineethmails • vineethmails

i tried the commands on the latest version 2.3.3 , still showing the same results.

• 0 views • link
written by vineethmails • vineethmails

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