Dear UCSC developers, I have the following problem. I try to upload a bam file in UCSC (http://genome.ucsc.edu/), just a one-read file. I have this sam-file: ======================== DD7DT8Q1:4:1106:19806:39174#AAGGAT 147 chrX 33055128 40 47M19797N4M1D10M39S = 33055121 -124 AGATGTGACAGAGAGTCCTGGAAGGTTTTGATTGCATTTTCTGAGAAGGAGATGTGACAGAGAGTCCTGGAAGGTTTTGATTGCATTTTCTGAGGTGTAC cgfeggggffgfgggggaggggggggggggggggggggggggggggggggggggggggggggggbggggggggggggggggggggggggggggggggggg MD:Z:45GT4^T0C9 NH:i:1 NM:i:3 SM:i:40 XQ:i:40 X2:i:0 XS:A:- ========================
I do the following: ======================== > samtools view -bt human.fa.fai test.sam >> test.bam > samtools sort test.bam test.sort (even though it's senseless in my case of > one read I still do this) > samtools index test.sort.bam ======================== Then I try to upload it like this to the UCSC: track type=bam name="My_BAM" bigDataUrl=http://barmsijs.lumc.nl/test.sort.bam And I get the following error: ======================== Error : buffer overflow, size 32, format: %s, buffer: 'chrgi|251831106|ref|NC_012920.1' ======================== Can anyone help me with this? I tried to find the solutions on the mailing list archives but found nothing suitable. I'd really appreciate your help. Thanks in advance! Cheers, Irina Pulyakhina, 1st year PhD student, The Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
