Flanking TSS region for reverse strand using biomaRt
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@kishor-tappita-2563
Last seen 8.1 years ago
Dear Group, I am using biomaRt to retrieve the flanking region from the TSS. I use the below statement for retrieving the 1000 bp upstream region from the TSS for yeast organism. seq=getSequence(id="R0010W",type="ensembl_gene_id",seqType="coding_gen e_flank",upstream=1000,mart = mart); Now my question is if the TSS is on reverse strand and I would like to retrive the 1000 bp upstream region what should be my command ???? Below is the command that I used.. seq=getSequence(id="R0020C",type="ensembl_gene_id",seqType="coding_gen e_flank",downstream=1000,mart = mart); Please let me know if I am doing it the right way... Thanks, Kishor
Yeast Organism biomaRt Yeast Organism biomaRt • 1.2k views
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Ania Lorenc ▴ 10
@ania-lorenc-4367
Last seen 8.1 years ago
Hello, I'm preparing a custom cdf for a custom SNP/CNV array. However,without success. Could someone suggest what might cause source this error? Thanks, Ania Lorenc Parsing file: MOUSEDIVm520650.CDF... Getting SNP probes... Organizing PM probes for SNPs... Getting SNP information... Organizing PM probes for CNVs... Getting sequences for SNPs... Getting sequences for CNVs... Merging sequence information for SNPs... Merging sequence information for CNVs... Creating Biostrings objects... Error in .charToXString(basetype, x, solved_SEW) : key 32 not in lookup table Calls: makePdInfoPackage ... XStringSet -> .charToXStringSet -> .charToXString -> .Call In addition: Warning messages: 1: In rm(cols, ok, colsOut, seq) : object 'ok' not found 2: In rm(cols, ok, colsOut, seq) : object 'ok' not found sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] pdInfoBuilder_1.14.1 oligo_1.14.0 oligoClasses_1.12.1 [4] affxparser_1.22.0 RSQLite_0.9-3 DBI_0.2-5 [7] Biobase_2.10.0 R.utils_1.5.7 R.oo_1.7.4 [10] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] Biostrings_2.18.0 IRanges_1.8.2 affyio_1.18.0 [4] preprocessCore_1.12.0 splines_2.12.0 > loaded via a namespace (and not attached): [1] tools_2.12.0
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Can you update your Biostrings and double check that your sequences include only valid characters (ATCG)? On 29 November 2010 12:28, Ania Lorenc <lorenc at="" evolbio.mpg.de=""> wrote: > Hello, > > I'm preparing a custom cdf for a custom SNP/CNV array. However,without > success. Could someone suggest what might cause source ?this error? > > Thanks, > > Ania Lorenc > > Parsing file: MOUSEDIVm520650.CDF... > Getting SNP probes... > Organizing PM probes for SNPs... > Getting SNP information... > Organizing PM probes for CNVs... > Getting sequences for SNPs... > Getting sequences for CNVs... > Merging sequence information for SNPs... > Merging sequence information for CNVs... > Creating Biostrings objects... > Error in .charToXString(basetype, x, solved_SEW) : key 32 not in lookup > table > Calls: makePdInfoPackage ... XStringSet -> .charToXStringSet -> > .charToXString -> .Call > In addition: Warning messages: > 1: In rm(cols, ok, colsOut, seq) : object 'ok' not found > 2: In rm(cols, ok, colsOut, seq) : object 'ok' not found > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] stats ? ? graphics ?grDevices datasets ?utils ? ? methods ? base > > other attached packages: > ?[1] pdInfoBuilder_1.14.1 oligo_1.14.0 ? ? ? ? oligoClasses_1.12.1 > ?[4] affxparser_1.22.0 ? ?RSQLite_0.9-3 ? ? ? ?DBI_0.2-5 > ?[7] Biobase_2.10.0 ? ? ? R.utils_1.5.7 ? ? ? ?R.oo_1.7.4 > [10] R.methodsS3_1.2.1 > > loaded via a namespace (and not attached): > [1] Biostrings_2.18.0 ? ? IRanges_1.8.2 ? ? ? ? affyio_1.18.0 > [4] preprocessCore_1.12.0 splines_2.12.0 >> > > loaded via a namespace (and not attached): > [1] tools_2.12.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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