Good Morning Yuan: There is no mechanism to change the coordinates in a SAM/BAM file. You can map your sequences to the genome reference sequence to obtain locations in the genome coordinates.
--Hiram ----- Original Message ----- From: "Yuan Hao" <[email protected]> To: [email protected] Sent: Monday, December 27, 2010 6:17:03 PM Subject: [Genome] How to view refSeq short reads alignment on UCSC Dear list, May I ask for some help in viewing short reads alignment to refSeq sequences instead of genomic sequences on UCSC. I have rna-seq reads aligned to refseq sequences from UCSC. In order to view the alignments on UCSC, I have to convert the refseq positions in my SAM/BAM files into genomic coordinates. Is there any way for me to reach this objective? I had a look at the 'refSeqAli.txt' table from UCSC, but haven't got a clue yet. I appreciate for any of your input! Kind regards, Yuan _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
