On Tue, Sep 28, 2010 at 10:50 AM, Benilton Carvalho <
beniltoncarvalho@gmail.com> wrote:

> very useful... thank you. b
>
> On 28 September 2010 15:22, Ivan Gregoretti <ivangreg@gmail.com> wrote:
> > Just for the purpose of documenting, this is your shortcut to get the
> > problem solved:
> >
> >
> http://picard.sourceforge.net/command-line-overview.shtml#ReplaceSamHeader
> >
>

Or samtools reheader (version 0.1.8 onward)

Sean


> >
> >
> >
> >
> > On Tue, Sep 28, 2010 at 10:15 AM, Benilton Carvalho
> > <beniltoncarvalho@gmail.com> wrote:
> >> Hi Ivan,
> >>
> >> thanks a lot...
> >>
> >> This happens to 2 files I have (that's why I think the problem is with
> >> the files)... So, the header (using samtools view -H) is concordant
> >> with Rsamtools...
> >>
> >> @SQ     SN:chr10        LN:135374737
> >> @SQ     SN:chr11        LN:0
> >> @SQ     SN:chr12        LN:0
> >> @SQ     SN:chr13        LN:0
> >> @SQ     SN:chr14        LN:0
> >> @SQ     SN:chr15        LN:0
> >> @SQ     SN:chr16        LN:0
> >> @SQ     SN:chr17        LN:0
> >> @SQ     SN:chr18        LN:0
> >> @SQ     SN:chr19        LN:0
> >> @SQ     SN:chr1 LN:0
> >> @SQ     SN:chr20        LN:0
> >> @SQ     SN:chr21        LN:46944323
> >> @SQ     SN:chr22        LN:0
> >> @SQ     SN:chr2 LN:0
> >> @SQ     SN:chr3 LN:0
> >> @SQ     SN:chr4 LN:0
> >> @SQ     SN:chr5 LN:0
> >> @SQ     SN:chr6 LN:0
> >> @SQ     SN:chr7 LN:0
> >> @SQ     SN:chr8 LN:0
> >> @SQ     SN:chr9 LN:0
> >> @SQ     SN:chrM LN:0
> >> @SQ     SN:chrX LN:0
> >> @SQ     SN:chrY LN:57772954
> >>
> >> So, the header seems to be the culprit...
> >>
> >> Thank you very much,
> >>
> >> b
> >>
> >>
> >> On 28 September 2010 15:06, Ivan Gregoretti <ivangreg@gmail.com> wrote:
> >>> Hi Benilton,
> >>>
> >>> Does this happen with all your BAM files?
> >>>
> >>> Check the header in the BAM file. For mouse, it should look like this:
> >>>
> >>> samtools view -H myfile.bam
> >>> @HD     VN:1.0  SO:coordinate
> >>> @SQ     SN:chr1 LN:197195432
> >>> @SQ     SN:chr2 LN:181748087
> >>> @SQ     SN:chr3 LN:159599783
> >>> @SQ     SN:chr4 LN:155630120
> >>> @SQ     SN:chr5 LN:152537259
> >>> @SQ     SN:chr6 LN:149517037
> >>> @SQ     SN:chr7 LN:152524553
> >>> @SQ     SN:chr8 LN:131738871
> >>> @SQ     SN:chr9 LN:124076172
> >>> @SQ     SN:chr10        LN:129993255
> >>> @SQ     SN:chr11        LN:121843856
> >>> @SQ     SN:chr12        LN:121257530
> >>> @SQ     SN:chr13        LN:120284312
> >>> @SQ     SN:chr14        LN:125194864
> >>> @SQ     SN:chr15        LN:103494974
> >>> @SQ     SN:chr16        LN:98319150
> >>> @SQ     SN:chr17        LN:95272651
> >>> @SQ     SN:chr18        LN:90772031
> >>> @SQ     SN:chr19        LN:61342430
> >>> @SQ     SN:chrX LN:166650296
> >>> @SQ     SN:chrY LN:15902555
> >>> @SQ     SN:chrM LN:16299
> >>> @SQ     SN:chr13_random LN:400311
> >>> @SQ     SN:chr16_random LN:3994
> >>> @SQ     SN:chr17_random LN:628739
> >>> @SQ     SN:chr1_random  LN:1231697
> >>> @SQ     SN:chr3_random  LN:41899
> >>> @SQ     SN:chr4_random  LN:160594
> >>> @SQ     SN:chr5_random  LN:357350
> >>> @SQ     SN:chr7_random  LN:362490
> >>> @SQ     SN:chr8_random  LN:849593
> >>> @SQ     SN:chr9_random  LN:449403
> >>> @SQ     SN:chrUn_random LN:5900358
> >>> @SQ     SN:chrX_random  LN:1785075
> >>> @SQ     SN:chrY_random  LN:58682461
> >>>
> >>> I suspect that you have a corrupt header.
> >>>
> >>> Ivan
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, Sep 28, 2010 at 9:28 AM, Benilton Carvalho
> >>> <beniltoncarvalho@gmail.com> wrote:
> >>>> Hi,
> >>>>
> >>>> I wonder if you guys could help me out understanding what the problem
> >>>> may be when reading in some BAM files I have...
> >>>>
> >>>> When viewing them with samtools, I get reads on chr6 (samtools view
> >>>> file.bam chr6)
> >>>>
> >>>> When using scanBam/scanBamHeader, I do not get any reads on chr6
> >>>> (latest RSamtools on 2.11.1, but same happens with the latest devel
> >>>> too).
> >>>>
> >>>> Suggestions on how to proceed in order to understand what may be going
> >>>> on (or what I may be missing)? My guess is that the files are
> >>>> corrupted, nothing strange comes up when using samtools...
> >>>>
> >>>> Thank you,
> >>>>
> >>>> benilton
> >>>>
> >>>> _______________________________________________
> >>>> Bioc-sig-sequencing mailing list
> >>>> Bioc-sig-sequencing@r-project.org
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >>>>
> >>>
> >>
> >
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>

	[[alternative HTML version deleted]]

