Hi Juliana, Selecting "sequence" in the Table Browser only ever outputs genomic (reference) sequence (apart from a few instances where select RNA and/or protein sequence is an option). This is the reason you only see "A".
On of our engineers looked at this one and commented: "The user is probably better off getting sequence straight from the SAM/BAM... for example, get SAM output from the Table Browser and look at the CIGAR and query sequence fields; or download the whole BAM file and use samtools (samtools.sourceforge.net). Run "samtools mpileup" to get usage instructions; a BED file can be passed in with "-l" to specify regions, and then the 5th column of output includes the query sequence bases found at that position. Other SAM/BAM toolsets (for example Broad's GATK) might have more direct solutions to the user's problem, samtools is just the one I'm familiar with." I hope that helps. If you need some additional info on the BAM/SAM file types, see here: http://genome.ucsc.edu/FAQ/FAQformat.html#format5.1 Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 11/28/11 12:43 PM, Juliana Morales wrote: > Dear UCSC Genome Browser Personnel, > > When I use the Table Browser with the following specs... > > Clade: Mammal > Genome: Human > Assembly: hg18 > Group: Denisova Assembly and Analysis > Track: Denisova > Table: bamSLDenisova > Define Regions: chr16:10,019,760-10,019,760 (for example) > Intersection: group: Variants and Repeats-track: SNPs130-Table_SNPs130 > Output format: sequence > Output type returned: plain text > > ...the output I get contains the allele of the reference human (A) as > opposed to the C which is visible when using the visual browser itself. > When I removed the intersection and simply attempted to get the output as > "Sequence > the sequence which is given to me (see below) has the reference human > allele at the position in question (chr16: 10019760). All of my results I > am getting where the Denisova differs from the Reference Human have this > same problem. Am I doing something wrong? I am just trying to get the > Denisova allele at the various SNP130 snps at the positions I am entering, > so could you please advise me? > > >> hg18_bamSLDenisova_C_M_SOLEXA-GA04_PE_JK_3003_3004:5:35:10988:4706#GTCGACT >> range=chr16:10019706-10019765 5'pad=0 3'pad=0 strand=+ repeatMasking=none > AAGAAGGTGGGGTTTCTGTGCTAGCACCAGAAGACACAAACTGGAGGCAG > CAATACCACT >> hg18_bamSLDenisova_C_M_SOLEXA-GA01_PEi_JK_3003:3:116:17181:9520#GTCGACT >> range=chr16:10019727-10019786 5'pad=0 3'pad=0 strand=+ repeatMasking=none > TAGCACCAGAAGACACAAACTGGAGGCAGCAATACCACTGCAGTTGATGT > GACAGAAGCC > > Sincerely, > > Rob Lowery > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
