Hi,
Does anyone has a script, that can be shared to create track hub for a list of files present in a directory and in its sub directories based upon the genome they belong to. The genome could be hg18, hg19, mm9, mm10 etc. Of course this genome information is already present in the name of bigwigs.
The naming convention that I have used is:
flowcell_lane_id_genome.bw
kindly help with a script.
Thank you
2 answers
I wrote the trackhub package to do exactly this. It allows you to flexibly configure and upload track hubs to UCSC. The README has an example that should take minimal editing to work for the use-case you describe.
I played with TrackHubs last year. See my blog: http://plindenbaum.blogspot.fr/2013/07/playing-with-ucsc-genome-browser-track.html
The script is hosted on github: https://github.com/lindenb/genomehub
•
written
by
Pierre Lindenbaum
Log in to answer this question.
-
Merging lots of csv files in on master one
written by psschlogl •
-
findPath using fastqs in sub-directories
written by kathrynm •
-
Mapping using UCSC and counting using RefSeq
written by Fawzi Yassine •
-
BIC-seq2 for detecting CNVs in mouse mm10-mapped WGS data
written by ivan.molodtsov •
-
UCSC ENCODE Broad histone modifications genome version
written by Rishikesh Lotke •
-
bigwig file in UCSC custom track
written by Ati •
-
ggbio package only works with h19 genome
written by tiago211287
-
A Non-Human Variants Data Analysis Error By Using Variants_Reduction.Pl
written by Tonyzeng •
-
How To Convert Chromosome Names Of Ensembl Annotation To The Ones Of Ucsc Refseq Database?
written by Ning-Yi Shao
-
Chromosome Position From Ucsc Genome Browser
written by Gjain
