<![CDATA[BOL: How to remove duplicates reads Ids ?]]> https://bioinformaticsonline.com/answers/view/32425/how-to-remove-duplicates-reads-ids? https://bioinformaticsonline.com/answers/view/32425/how-to-remove-duplicates-reads-ids Wed, 03 May 2017 08:41:11 -0500 https://bioinformaticsonline.com/answers/view/32425/how-to-remove-duplicates-reads-ids <![CDATA[How to remove duplicates reads Ids ?]]>
I mapped reads with
bwa mem -M -t 40 allCombinedFinalSet.fa Seq.R1.fastq Seq.R2.fastq > aln.sam

Extracted the mapped reads

samtools view -f 0x2 -b aln.bam > output.bam

Extracted the fastq

bamToFastq -i output.bam -fq R1.fq -fq2 R2.fq 

grep @HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1 R1.fq             []
@HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
@HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1
@HISEQ578:1035:HJ2KCBCXX:1:1104:14672:39678/1

I notice it has duplicated ....

I think this because read was mapped twice (i.e. BWAmem).

I tried fastuniq but it does not remove the duplicated reads.

Can you please help me to remove duplicated reads from fastq files.

]]> Abhimanyu Singh