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  • 1000g sequence reads PE or SE?

    I have trouble understand which reads are single reads and which are pair ended reads

    For example, there are three files in

    ftp://ftp.1000genomes.ebi.ac.uk/vol1...sequence_read/

    SRR035330_1.filt.fastq.gz
    SRR035330_2.filt.fastq.gz
    SRR035330.filt.fastq.gz

    I checked the sequence index and they are all supposedly PAIR_ENDED. I think SRR035330_1.filt.fastq.gz and SRR035330_2.filt.fastq.gz constitute one pair. I think I can run them thru bwa to get two sai files and go from there.

    But what is SRR035330.filt.fastq.gz??? Is it really pair ended reads? Or is it single reads?

    Thanks a lot!

  • #2
    The third file is unpaired. I'm not sure which genomes you are using but many are sequenced using multiple platforms. For example, some are sequenced using SOLID and ILLUMINA.

    Comment


    • #3
      Thanks for your reply. Suppose I want to generate a single bam file from them. Is this the right way to do this?

      bwa aln -t 6 hg19.fa SRR035330.filt.fastq.gz > 0.sai
      bwa aln -t 6 hg19.fa SRR035330_1.filt.fastq.gz > 1.sai
      bwa aln -t 6 hg19.fa SRR035330_2.filt.fastq.gz > 2.sai
      bwa samse hg19.fa 0.sai SRR035330.filt.fastq.gz | samtools view -bS - > se.bam
      bwa sampe hg19.fa 1.sai 2.sai SRR035330_1.filt.fastq.gz SRR035330_2.filt.fastq.gz | samtools view -bS - > pe.bam
      samtools merge SRR035330.bam se.bam pe.bam

      Comment


      • #4
        That's the idea. And then of course sort and mark duplicates....

        Comment


        • #5
          Ah. Now that I think about it. I think the SRR035330 run is a pair ended one. But for some reasons, only one end is sequenced for some fragments. This explains why the SRR035330.filt.fastq.gz is much smaller than the other two files.

          Did I describe the situation correctly?

          Comment


          • #6
            This is possible too. Sometimes you get unpaired reads from PE sequencing.

            Comment

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