paired reads have different names

Question

[daffodil]

Dear all I have downloaded fastq file and run BWA mem.

~/bwa/bwa/./bwa mem -t 24 \
    -R '@RG\tID:s99\tSM:Ex99\tPL:Illumina\tPU:Hiseq2500' \
    -M /home/hg19/hg19.fa \
    gfan787_1.fastq.gz gfan787_2.fastq.gz >g.sam

After that I took this message:

paired reads have different names: "PRWES615:444:HYMK3DSXY:3:1131:6280:20415", "PRWES615:444:HYMK3DSXY:3:1131:12255:20400"

It should be appreciated if you could let me know how I can solve it. Best

[Pierre Lindenbaum]

you're using the wrong FASTQ files or you preprocessed them without keeping the original order.

[GenoMax]

PRWES615:444:HYMK3DSXY:3:

Based on this part of read name it looks like it it the same flowcell/lane so most likely the two data files were separately trimmed.

daffodil : You can use repair.sh from BBMap suite to re-sync your data files and remove singleton/orphan reads.

repair.sh in1=R1.fastq in2=R2.fastq out1=clean_R1.fastq out2=clean_R2.fastq outsingle=singleton.fastq