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  • swbarnes2
    replied
    Well, don't merge them into 1 file, that's just throwing away real paired information.

    You want all of the read 1 data in one fastq, and all the read 2 data in a second. Just make sure that the nth entry in the first fastq has the same read name as the nth read in file 2.

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  • nayshool@gmail.com
    replied
    problem solved

    Originally posted by swbarnes2 View Post
    The .bam from bgi reports the exact same number of read 1 reads as read 2 reads. Yours does not. Are you sure that giving it 4 fastq files at once is the proper way to use bwa mem? I wonder if it is just ignoring those last two files. Maybe you could spot-check to see if read names from those fastqs are in your .bam
    Well i merged the 4 fastQ into one file and it did the trick. It's appear that BWA-MEM ignored from the last 2 files as you said. I got the right size of BAMs after that . Thank you swbarnes2 very much for your help!

    Leave a comment:


  • swbarnes2
    replied
    The .bam from bgi reports the exact same number of read 1 reads as read 2 reads. Yours does not. Are you sure that giving it 4 fastq files at once is the proper way to use bwa mem? I wonder if it is just ignoring those last two files. Maybe you could spot-check to see if read names from those fastqs are in your .bam

    Leave a comment:


  • nayshool@gmail.com
    replied
    thank you. I have mislabled the flagstat ouputs, I have change it. BGI have more reads.

    Originally posted by dpryan View Post
    Unless you mislabeled the flagstat output, it looks like your results contain about twice as many alignments as those from BGI, though that could be due to yours containing multiple copies of multimappers while BGI's doesn't. In general, you'd need to look at how they aligned things and that will likely tell you why there's a difference.

    Leave a comment:


  • nayshool@gmail.com
    replied
    Sorry for the duplicate, won't happen again..

    I'll try to remove the question from BioStars

    Originally posted by dpryan View Post
    BTW, please don't cross post on both here and biostars, it creates duplicate work from the community.

    Leave a comment:


  • maubp
    replied
    Does either set of BAM file include unmapped read pairs? 'samtools idxstats example.bam' might help answer this.

    P.S. Duplicate question was https://www.biostars.org/p/108537/

    Leave a comment:


  • dpryan
    replied
    BTW, please don't cross post on both here and biostars, it creates duplicate work from the community.

    Leave a comment:


  • dpryan
    replied
    Unless you mislabeled the flagstat output, it looks like your results contain about twice as many alignments as those from BGI, though that could be due to yours containing multiple copies of multimappers while BGI's doesn't. In general, you'd need to look at how they aligned things and that will likely tell you why there's a difference.

    Leave a comment:


  • nayshool@gmail.com
    started a topic Problem with alignment

    Problem with alignment

    Hello everyone!

    We have received from BGI china a few samples we sent for exome sequence + Basic analysis. We got the fastQ files and BAM files. I have made my own BAM files using BWA and Picard tools using the following commends:

    BWA:
    bwa mem human_g1k_v37.fasta file1.fq.gz file2.fq.gz file3.fq.gz file4.fq.gz > result.sam

    PICARD:
    java -jar SortSam.jar I=result.sam O=result.bam SORT_ORDER=coordinate

    The size of the files that I got (2Gb) , was about a half from the BAM files BGI (4.2 Gb) sent me.
    Here are the samtools flagstat results for both files:

    my BAM file:

    [[email protected] VA6]$ samtools flagstat result.bam
    28842836 + 0 in total (QC-passed reads + QC-failed reads)
    0 + 0 duplicates
    28824861 + 0 mapped (99.94%:-nan%)
    28842836 + 0 paired in sequencing
    14423043 + 0 read1
    14419793 + 0 read2
    28593748 + 0 properly paired (99.14%:-nan%)
    28814004 + 0 with itself and mate mapped
    10857 + 0 singletons (0.04%:-nan%)
    165631 + 0 with mate mapped to a different chr
    131466 + 0 with mate mapped to a different chr (mapQ>=5)



    BGI BAM File:

    [[email protected] result_alignment]$ samtools flagstat VA6.rmdup.bam
    57668392 + 0 in total (QC-passed reads + QC-failed reads)
    3039053 + 0 duplicates
    57369744 + 0 mapped (99.48%:-nan%)
    57668392 + 0 paired in sequencing
    28834196 + 0 read1
    28834196 + 0 read2
    56991680 + 0 properly paired (98.83%:-nan%)
    57273460 + 0 with itself and mate mapped
    96284 + 0 singletons (0.17%:-nan%)
    198072 + 0 with mate mapped to a different chr
    181774 + 0 with mate mapped to a different chr (mapQ>=5


    why does half of my reads disappear? How can I solve this problem?

    Thank you,

    Omri
    Last edited by [email protected]; 08-05-2014, 05:04 AM.
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