Hi Devon,
Great! Thanks a lot for this list!
On Thu, May 19, 2016 at 5:18 PM, Devon Ryan <dpr...@dpryan.com> wrote:
> You can largely just swap the names. Here is a file with the
> chromosome name conversions:
>
> https://github.com/dpryan79/ChromosomeMappings/blob/master/GRCh37_ensembl2UCSC.txt
>
> Note that there are some contigs/alternate haplotypes present in
> Ensembl genomes that are either absent in the UCSC release or merged
> together (those chr?_random things). You'll have to just get rid of
> them.
>
> 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 2:10 PM, Bayazit Yunusbayev <yunu...@gmail.com>
> wrote:
> > 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 is UCSC's variant of the 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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