Hello, I was wondering if you could help me out or at least point me in the right direction.
I'm trying to generate coverage plots for my Solexa data on Arabidopsis, but in order to do so I need a file containing the chromosomes and their lengths. A file similar to this example for humans: <Chromosome> / <Chromosome Length> / <file source> chr1 249250621 /gbdb/hg19/hg19.2bit chr2 243199373 /gbdb/hg19/hg19.2bit chr3 198022430 /gbdb/hg19/hg19.2bit chr4 191154276 /gbdb/hg19/hg19.2bit chr5 180915260 /gbdb/hg19/hg19.2bit chr6 171115067 /gbdb/hg19/hg19.2bit chr7 159138663 /gbdb/hg19/hg19.2bit chrX 155270560 /gbdb/hg19/hg19.2bit chr8 146364022 /gbdb/hg19/hg19.2bit chr9 141213431 /gbdb/hg19/hg19.2bit chr10 135534747 /gbdb/hg19/hg19.2bit chr11 135006516 /gbdb/hg19/hg19.2bit chr12 133851895 /gbdb/hg19/hg19.2bit chr13 115169878 /gbdb/hg19/hg19.2bit chr14 107349540 /gbdb/hg19/hg19.2bit chr15 102531392 /gbdb/hg19/hg19.2bit chr16 90354753 /gbdb/hg19/hg19.2bit chr17 81195210 /gbdb/hg19/hg19.2bit chr18 78077248 /gbdb/hg19/hg19.2bit chr20 63025520 /gbdb/hg19/hg19.2bit chrY 59373566 /gbdb/hg19/hg19.2bit chr19 59128983 /gbdb/hg19/hg19.2bit chr22 51304566 /gbdb/hg19/hg19.2bit chr21 48129895 /gbdb/hg19/hg19.2bit chr6_ssto_hap7 4928567 /gbdb/hg19/hg19.2bit chr6_mcf_hap5 4833398 /gbdb/hg19/hg19.2bit chr6_cox_hap2 4795371 /gbdb/hg19/hg19.2bit chr6_mann_hap4 4683263 /gbdb/hg19/hg19.2bit chr6_apd_hap1 4622290 /gbdb/hg19/hg19.2bit chr6_qbl_hap6 4611984 /gbdb/hg19/hg19.2bit chr6_dbb_hap3 4610396 /gbdb/hg19/hg19.2bit chr17_ctg5_hap1 1680828 /gbdb/hg19/hg19.2bit chr4_ctg9_hap1 590426 /gbdb/hg19/hg19.2bit chr1_gl000192_random 547496 /gbdb/hg19/hg19.2bit chrUn_gl000225 211173 /gbdb/hg19/hg19.2bit chr4_gl000194_random 191469 /gbdb/hg19/hg19.2bit chr4_gl000193_random 189789 /gbdb/hg19/hg19.2bit chr9_gl000200_random 187035 /gbdb/hg19/hg19.2bit chrUn_gl000222 186861 /gbdb/hg19/hg19.2bit chrUn_gl000212 186858 /gbdb/hg19/hg19.2bit chr7_gl000195_random 182896 /gbdb/hg19/hg19.2bit chrUn_gl000223 180455 /gbdb/hg19/hg19.2bit chrUn_gl000224 179693 /gbdb/hg19/hg19.2bit chrUn_gl000219 179198 /gbdb/hg19/hg19.2bit chr17_gl000205_random 174588 /gbdb/hg19/hg19.2bit chrUn_gl000215 172545 /gbdb/hg19/hg19.2bit chrUn_gl000216 172294 /gbdb/hg19/hg19.2bit chrUn_gl000217 172149 /gbdb/hg19/hg19.2bit chr9_gl000199_random 169874 /gbdb/hg19/hg19.2bit I would try generating it myself, but I don't understand what the later regions represent. For example, chrUn_glXXXXXX, in the above case, but they differ in other organisms. I tried generating a file simply with chr1, chr2, ch3, ch4, chr5, chrC, and chrM but it did not work. @TAIR: I tried locating this or a similar file on your FTP and was unsuccessful in doing so. @UCSC: I found the Arabidopsis mirror site, but it doesn't offer downloads specifically for Arabidopsis, but I was able to find this file (chromInfo.txt) for many of the other organisms in your FTP. If either of you could assist me with this issue it would be greatly appreciated. Generating coverage plots of our data has been in the cards for a while and upon learning how to generate them, not having this file is causing a set back. Thank you very much for your time. -Brandon Brandon Dinwiddie University of Missouri - Kansas City _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
