Dear Brooke, dear all, thanks a lot for your fast help,
cheers, Carsten > Hi Carsten, > > These questions about SAM format should really be directed to the > samtools-help list rather than the Genome Browser help list. > > However, one of our engineers explained what you are seeing: > > "This is a SAM/BAM quirk: the strand flag is only a historical note. > The query sequence is reverse-complemented if necessary to match the > forward strand of the target/reference. Thus the CIGAR string marches > forward through the query sequence and the reference/target sequence." > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 11/24/11 8:37 AM, Carsten Raabe wrote: >> Dear Pauline, dear all, >> >> I am afraid I am still not getting it correctly. According to what I >> have read and explained in last mail I would expect that Flag 16 in >> column2 stands for reverse matching (*>>>* i.e. the RNA is encoded on >> the reverse strand). In the examples below I challenged the annotation >> within the sam file by blating the read against the human genome. >> Interestingly there is no difference in orientation of the read >> irrespective of the column2 Flag (>>> 16 or 0). Would that mean that >> the >> sequence in the sam file irrespective of true read annotation always >> resembles the sense strand ?? If correct this would make me conclude >> that the coordinate in column4 in case of Flag 16 stands for the 3' >> most position of the read. >> >> >> Thanks a lot in advance..... >> >> Carsten >> >> 9990-80 *16* chr11 *59394452* 255 41M * >> 0 0 AGTTGCCCTACGTGTGCCACTCACGACAGAAGCCCTTTTTT >> IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:41 >> NM:i:0 YG >> :i:1 YC:Z:255,0,255 >> *>>>> UCSC browser* 9990-80 41 1 41 41 100.0% 11 *+ 59394452* >> 59394492 41 >> >> 9994-80 *16* chr2 *133012312 * 255 34M * 0 >> 0 TGGCTGAACGCCACTTGTCCCTCTAAGAAGTTGG >> IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:34 NM:i:0 YG:i:1 >> YC:Z:255,0 >> ,255 >> *>>>> UCSC browser* 9994-80 34 1 34 34 100.0% 2 *+* *133012312* >> 133012345 34 >> >> 9999-80 *0 * chr13 *92003326 * 255 25M * >> 0 0 TAAAGTGCTTATAGTGCAGGTAATT >> IIIIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:22G1G0 NM:i:2 YG:i:1 >> YC:Z:255,0,255 >> >> *>>> UCSC browser* 9999-80 22 1 22 25 100.0% 13 *+* *92003326* >> 92003347 22 >> >> 9990-80 *16* chr11 *59394452* 255 41M * >> 0 0 AGTTGCCCTACGTGTGCCACTCACGACAGAAGCCCTTTTTT >> IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:41 >> NM:i:0 YG >> :i:1 YC:Z:255,0,255 >> >> *>>>> UCSC browser* 9990-80 41 1 41 41 100.0% 11*+* *59394452* >> 59394492 41 >> >> 9965-80 *0 * chr13 *92002872* 255 23M * >> 0 0 CAAAGTGCNTACAGTGCAGGTAG IIIIIIIIIIIIIIIIIIIIIII XA:i:1 >> MD:Z:8T14 NM:i:1 YG:i:1 YC:Z:255,0,255 >> >> *>>>> UCSC browser *9965-80 22 1 23 23 100.0% 13 *+* *92002872* >> 92002894 23 >> >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
