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  • Bfast alignement with paired end reads in separate files

    Hello,

    I am dealing with Illumina paired end reads (100 + 100) and I am trying to align them by using bfast. The point is that they are in separate files, and I am wondering which is the best way to proceed. My attempt:

    1. bfast match:
    Code:
    bfast match -f hg19.fa -A 0  -g -r reads_file_pair_1.fastq.gz -i 1 -K 8 -M 128 -w 0 > pair_1.bmf
    bfast match -f hg19.fa -A 0  -g -r reads_file_pair_2.fastq.gz -i 1 -K 8 -M 128 -w 0 > pair_2.bmf
    2. bfast localalign:

    Code:
    bfast localalign -f hg19.fa -m pair_1.bmf -m pair_2.bmf -n 4 -A 0 -U > sample.baf
    3. bfast postprocess

    Code:
    bfast postprocess -i sample.baf -f hg19.fa -a 3 -z -A 0 -R -O 1 -n 4 -U | gzip > sample.sam.gz
    I am concerned specially in step 2; I am used to use two .bmf files (one per paired-end) in the bfast localign command when they have been outputted by the bfast bwaaln command (using "-1" and "-2" arguments), but I've never done so with bafst match output files.

    Tahnk you very much in advance,

  • #2
    Test it out to see what happens. You should be pleasantly surprised.

    Comment


    • #3
      Unfortunately, I think it does not work, the bfast localign seems to take into account only the second passed .bmf file:

      Code:
      bfast localalign -f hg19.fasta -m dummy_p1.bmf -m dummy_p2.bmf -n 4 -A 0 -U > dummy.baf
      The stdoutput when executing this command:
      Code:
      ************************************************************
      Printing Program Parameters:
      programMode:			[ExecuteProgram]
      fastaFileName:			hg19.fasta
      matchFileName:			dummy_p2.bmf
      matchFileNameOne:		[Not Using]
      matchFileNameTwo:		[Not Using]
      scoringMatrixFileName:		[Not Using]
      ungapped:			[Not Using]
      unconstrained:			[Using]
      space:				[NT Space]
      startReadNum:			1
      endReadNum:			2147483647
      offsetLength:			20
      maxNumMatches:			384
      avgMismatchQuality:		10
      numThreads:			4
      queueLength:			10000
      timing:				[Not Using]
      ************************************************************
      And effectively, I've checked the .sam file obtained after the bfast postprocess step and the aligned reads are only those of the second "end-reads" file.

      Am I doing something wrong? Btw, I am using the bfast+bwa-0.6.4e.

      Thanks,
      David

      Comment

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