Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

            Latest Articles

            Collapse

            • seqadmin
              Exploring the Dynamics of the Tumor Microenvironment
              by seqadmin




              The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
              07-08-2024, 03:19 PM
            • seqadmin
              Exploring Human Diversity Through Large-Scale Omics
              by seqadmin


              In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
              06-25-2024, 06:43 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Yesterday, 05:49 AM
            0 responses
            12 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-15-2024, 06:53 AM
            0 responses
            23 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-10-2024, 07:30 AM
            0 responses
            36 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-03-2024, 09:45 AM
            0 responses
            204 views
            0 likes
            Last Post seqadmin  
            Working...
            X