[Bioc-sig-seq] different results between Rsamtools and samtools

[Ivan Gregoretti]

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 at 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 at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>