Hi Devon,
Thank you very much for your help with this! I did not know it refers to a
telomeric region - could never guess it.
Although hg19
<http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=12836192&chromInfoPage=> is
UCSC's variant of the GRCh37
<http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/#GRCh37>
assembly, I am not sure whether I can simply replace 'chr1' with '1' - I
am reading about this right now.
Thank you!
On Thu, May 19, 2016 at 4:13 PM, Devon Ryan <dpr...@dpryan.com> wrote:
> 3:1000-2000 is unlikely to have any reads, it's a hard-masked
> telomere. As you surmised, your problem is using a BED file with UCSC
> chromosome names and a BAM file with Ensembl chromosome names. If you
> fix that then you should get reasonable results.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Thu, May 19, 2016 at 12:51 PM, Bayazit Yunusbayev <yunu...@gmail.com>
> wrote:
> > Dear All,
> >
> > I have a BAM file with reads from full genome sequencing
> >
> > and I wanted to extract only reads that match exome sequencing reads
> >
> > stored in my bed file.
> >
> > 1) here is the command that I used:
> >
> > samtools view -b -L CTR9_FEB2015.merged.realigned.bed V54120.bam -o
> > exom.V54120.bam
> >
> > So I got bam file that has only header lines
> >
> > when checked using: samtools view -H exom.V54120.bam
> >
> > but no reads! when trying : samtools view exom.V54120.bam
> >
> > and indeed it is very small in size (5.4 Kb)
> >
> >
> > I am new to samtools and below is my short investigation which, however,
> did
> > not help ;(
> >
> > I wonder whether I am missing something in my commands? Could anyone
> help me
> > with this?
> >
> > Thank you!
> >
> >
> > First I tried to check whether anything can be retrieved from the bam
> file:
> >
> > samtools view V54120.bam chr1:1000-2000
> >
> > and got the following error message:
> >
> > [main_samview] region "chr1:1000-2000" specifies an unknown reference
> name.
> > Continue anyway.
> >
> >
> > Then I checked chromosome names:
> >
> > samtools view -H /gpfs/rocket/gv/V54120.bam | awk '/@SQ/'
> > @SQ SN:1 LN:249250621 UR:
> http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta
> AS:GRCh37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo
> > Sapiens
> > @SQ SN:2 LN:243199373 UR:
> http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta
> AS:GRCh37 M5:a0d9851da00400dec1098a9255ac712e SP:Homo
> > Sapiens
> >
> >
> > Then assuming that 'chr1' should be '1',I tried:
> >
> > samtools view V54120.bam 3:1000-2000
> >
> > this produced nothing ;(
> >
> > no errors and no output to standard output
> >
> >
> >
> >
> >
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