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 >> > >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > Mobile security can be enabling, not merely restricting. Employees who >> > bring their own devices (BYOD) to work are irked by the imposition of >> > MDM >> > restrictions. Mobile Device Manager Plus allows you to control only the >> > apps on BYO-devices by containerizing them, leaving personal data >> > untouched! >> > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j >> > _______________________________________________ >> > Samtools-help mailing list >> > Samtools-help@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/samtools-help >> > > > ------------------------------------------------------------------------------ Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
