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

[Benilton Carvalho]

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 <ivangreg at gmail.com> 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
> <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
>>
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>