Re: [Bio-bwa-help] wrong mapping

[Shawn D. <sdr...@sa...>]

Both alignments have a flag of 4 which means "unaligned". So in terms of
the way those alignments would be interpreted by any downstream tools they
are unaligned. I don't know the details but things happen at different
stages within BWA so at times their can be seemingly conflicting info in an
alignment however the flag field is trustworthy.  I believe the SAM spec
says if the flag is 4 you shouldn't trust any other fields. That appears to
be good advise in this case.
On Jul 17, 2014 3:13 AM, "Cloelia Dard-Dascot" <
clo...@cg...> wrote:

> Hi
> i found out a weird behaving of BWA where it maps on the wrong part
>
> Here my reads which cause the problem pb.fastq:
> @M01342:47:000000000-A9VMJ:1:2110:28593:14009 1:N:0:1
> ATCGGACCAGGCTTCATTCCC
> +
> CBCCCCCCCFCCGGGGGGGGG
> @M01342:47:000000000-A9VMJ:1:2112:10072:14449 1:N:0:1
> ATCGGACCAGGCTTCATTCCC
> +
> AAABABBBBFAAFGGGGGGGG
>
> here is my reference genome brassica_pb.fa (actually they are micro RNA
> but it should work also, right?)
>  >bna-miR167c_MIMAT0005628_Brassica_napus_miR167c
> TGAAGCTGCCAGCATGATCTA
>  >bna-miR166a_MIMAT0005629_Brassica_napus_miR166a
> TCGGACCAGGCTTCATTCCCC
>
> here are my commands:
> /home/ctuser/Documents/programmes/bwa-0.7.10/bwa index brassica_pb.fa
> /home/ctuser/Documents/programmes/bwa-0.7.10/bwa aln -t 12 -n 0 -k 0
> brassica_pb.fa pb.fastq > ./res_BWA_pb_newVersion/pb.sai
> /home/ctuser/Documents/programmes/bwa-0.7.10/bwa samse brassica_pb.fa
> ./res_BWA_pb_newVersion/pb.sai $f > ./res_BWA_pb_newVersion/pb.sam
>
> here is my sam file:
> @SQ SN:bna-miR167c_MIMAT0005628_Brassica_napus_miR167c LN:21
> @SQ SN:bna-miR166a_MIMAT0005629_Brassica_napus_miR166a LN:21
> @PG ID:bwa PN:bwa VN:0.7.10-r789
> CL:/home/ctuser/Documents/programmes/bwa-0.7.10/bwa samse brassica_pb.fa
> ./res_BWA_pb_newVersion/pb.sai pb.fastq
> M01342:47:000000000-A9VMJ:1:2110:28593:14009 4
> bna-miR167c_MIMAT0005628_Brassica_napus_miR167c 21 25 21M * 0 0
> ATCGGACCAGGCTTCATTCCC CBCCCCCCCFCCGGGGGGGGG XT:A:U NM:i:0 X0:i:1 X1:i:0
> XM:i:0 XO:i:0 XG:i:0 MD:Z:21
> M01342:47:000000000-A9VMJ:1:2112:10072:14449 4
> bna-miR167c_MIMAT0005628_Brassica_napus_miR167c 21 25 21M * 0 0
> ATCGGACCAGGCTTCATTCCC AAABABBBBFAAFGGGGGGGG XT:A:U NM:i:0 X0:i:1 X1:i:0
> XM:i:0 XO:i:0 XG:i:0 MD:Z:21
>
> we can see that both of the reads have been mapped to the first mir but
> it should not have been mapped at all (or maybe to the second mir but I
> have put into parameter no mismatch)!!
> I tried three different versions of BWA (0.7.5, 0.6.1 and 0.7.10) but
> same behaviour.
> Did I do something wrong?
> I must say it usually work fine and found the right mir but for two
> cases includind this one, it found the mir just before the right one. Is
> there a problem of length?
> Thank for any help
>
>
>
>
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