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
