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 > > Ivan > > > > > 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
