you did not understand what I wanted to say..........

I map raw reads to CDS transcripts not on genome sequences.

But some of the gene sequences is missing in these CDS transcripts.

So when I map raw reads to these CDS, some pair end reads do not able to map.

I want to extract to those pair end reads in which BOTH READS of Pair not able to map to CDS.

For that I used below cammand line:

Cammand Lines:

For BWA indexing /home/yog/software/bwa-0.7.15/bwa index -p Radish_index Radish_cds.fasta

BWA Cammand /home/yog/software/bwa-0.7.15/bwa mem Radish_index forward_216_5W_Ca1.fastq reverse_216_5W_Ca1.fastq >216_5W_Ca1.sam

Convert Sam to BAM /home/yog/software/samtools-1.3.1/samtools view -bS 216_5W_Ca1.sam > 216_5W_Ca1.bam

Extract Unmapped Reads: /home/yog/software/samtools-1.3.1/samtools view -b -f 4 216_5W_Ca1.bam > unmap_216_5W_Ca1.bam

To convert bam to Fastq File: /home/yog/software/samtools-1.3.1/samtools sort -n unmap_Ca1.bam -o unmap_216_5W_Ca1._resorted

/home/yog/software/bedtools2/bin/bamToFastq -i unmap_Ca1._resorted -fq Unmap_Ca1_read1.fastq -fq2 Unmap_Ca1_read2.fastq

But when last cammnd line write R1 and R2 reads it shows some warning on screen:

WARNING: Query PC168224:127:C98A1ANXX:1:2316:21235:23135 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping. WARNING: Query PC168224:127:C98A1ANXX:1:2316:21236:13229 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping. *WARNING: Query PC168224:127:C98A1ANXX:1:2316:21237:66490 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

So I am asking is there I am making any mistake?