Question: Align paired and unpaired reads simultaneously using Bowtie2?
gravatar for xiaozhongzhiping
6 months ago by
xiaozhongzhiping0 wrote:

I have a MeatG library, which was sequenced by two times. The first time, we got unpaired reads (i.e., unpaired.fastq); while we got interlaced forward and reverse paired-end reads (i.e., interlaced-paired.fastq) for the 2nd time. Since they are from the same library, I assembled them together and got the assembled scaffolds. Now I would like to align both of them (unpaired and interlaced paired reads) simultaneously to the assembled contigs using Bowtie2 version to get one .sam file. Can Bowtie2 do this? Any suggestions are appreciated!

I tried the following two scripts, the results for both were same. So for the first script, only the paired reads are mapped.

bowtie2 -q --phred33 --end-to-end --sensitive -p 12 -I 0 -X 2000 --no-unal -x bowtie2-db/CBIW --interleaved interlaced-paired.fastq -U unpaired.fastq | samtools view -Sb - > output.bam

bowtie2 -q --phred33 --end-to-end --sensitive -p 12 -I 0 -X 2000 --no-unal -x bowtie2-db/CBIW --interleaved interlaced-paired.fastq | samtools view -Sb - > output.bam

See the align result:

Building a SMALL index

35388893 reads; of these:

  35388893 (100.00%) were paired; of these:

11580370 (32.72%) aligned concordantly 0 times

23621928 (66.75%) aligned concordantly exactly 1 time

186595 (0.53%) aligned concordantly >1 times

11580370 pairs aligned concordantly 0 times; of these:

    101972 (0.88%) aligned discordantly 1 time

    11478398 pairs aligned 0 times concordantly or discordantly; of these:

        22956796 mates make up the pairs; of these:

            22513992 (98.07%) aligned 0 times

            432094 (1.88%) aligned exactly 1 time

            10710 (0.05%) aligned >1 times

68.19% overall alignment rate
alignment • 659 views
ADD COMMENTlink modified 6 months ago by genomax62k • written 6 months ago by xiaozhongzhiping0
gravatar for h.mon
6 months ago by
h.mon23k wrote:

I don't think Bowtie2 can map paired- and single-end reads simultaneously, but you can merge both mappings with samtools. BWA can map map a mix of interleaved paired reads and single reads, if you concatenate both files and keep single reads at the end.

Use samtools sort to sort each bam by position, then samtools merge to merge the sorted bams into one.

If having a sorted bam is not important, you can just use samtools cat.

ADD COMMENTlink modified 6 months ago • written 6 months ago by h.mon23k

Thanks. I followed your suggestions using samtools sort and merge. It works well.

ADD REPLYlink written 5 months ago by xiaozhongzhiping0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1374 users visited in the last hour