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 220.127.116.11 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