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  • adaptivegenome
    replied
    This is possible too. Sometimes you get unpaired reads from PE sequencing.

    Leave a comment:


  • ymc
    replied
    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?

    Leave a comment:


  • adaptivegenome
    replied
    That's the idea. And then of course sort and mark duplicates....

    Leave a comment:


  • ymc
    replied
    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

    Leave a comment:


  • adaptivegenome
    replied
    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.

    Leave a comment:


  • ymc
    started a topic 1000g sequence reads PE or SE?

    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!

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