Hello, everyone. I have uploaded two custom tracks from ChIP-sequencing experiments at separate times, one with nearly three million objects, and one of approximately 800K. A curious thing happened on the way to the forum, using either hg18 or hg19.
For the larger file: reads are only mapped to the very beginning of each chromosome, with the exception of the acrocentric ones (13, 14, 15, 21, 22) - and always to the same point. In this case, they are visible to position 8,388,500, and I have the option to see them in dense, squish, full, etc. However, if I navigate to 8,388,600, the mapped reads to 8,388,500, no matter how large or small I make the window, will display only in dense format, and of course, nothing appears toward the higher coordinates. For the smaller file, a different but equally curious thing happens: Reads are mapped continuously on chromosomes 1 to 5 until position chr5:165,467,700 - and no more reads are mapped anywhere. However, when I straddle the end-point, I see the last reads still in whatever type of density I want (squish, usually). Both files have an approximately even coverage of reads over all chromosomes and indeed have reads on chrX, chrY and even chrM (none of the chrM ones are mapped at all). Nothing seems to differentiate in the concatenation between the last line of eg. chr1 reads and the first of chr2. Thank you very much in advance for any light you can shed on this. Sincerely, Heather Etchevers -- Heather C. Etchevers, Ph.D. 80% of the time: INSERM U563, CPTP Hôpital Purpan Place du Dr Baylac 31300 Toulouse, France tel : +33 562 744587 20% of the time: INSERM U781 Hôpital Necker (Lavoisier 2) 149 rue de Sèvres 75015 Paris, France tel : +33 144 494000 poste 97838 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
