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  • Is it possible to map small number of reads with bwa?

    I created two fastqs with nine reads each. Then I ran them thru bwa sampe but only one end is aligned. I looked at the error message. It seems to me the problem might be due to bwa's inability to estimate insert size in this case. Is it possible for us to tell bwa the insert size? I tried -a 1000 but it didn't work....

    [bwa_sai2sam_pe_core] convert to sequence coordinate...
    [infer_isize] fail to infer insert size: too few good pairs
    [bwa_sai2sam_pe_core] time elapses: 2.00 sec
    [bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
    [bwa_sai2sam_pe_core] align unmapped mate...
    [bwa_sai2sam_pe_core] time elapses: 0.31 sec
    [bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec
    [bwa_sai2sam_pe_core] print alignments... 0.03 sec
    [bwa_sai2sam_pe_core] 9 sequences have been processed.
    [main] Version: 0.6.1-r104
    [main] CMD: bwa sampe -r @RG\tID:exomeID\tLB:exomeLB\tSM:exomeSM\tPL:illumina\tPU:exomePU -a 2000 ../exome/human_g1k_v37.fasta 1.sai 2.sai dqa_1.fq dqa_2.fq
    [main] Real time: 2.583 sec; CPU: 2.348 sec
    [samopen] SAM header is present: 84 sequences.

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