On Tue, Sep 28, 2010 at 10:50 AM, Benilton Carvalho < [email protected]> wrote:
> very useful... thank you. b > > On 28 September 2010 15:22, Ivan Gregoretti <[email protected]> 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 > > <[email protected]> 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 <[email protected]> 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 > >>> <[email protected]> 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 > >>>> [email protected] > >>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > >>>> > >>> > >> > > > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
