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
