The goal is to display the results of measurement of expression (amount of mRNA) by RNA-seq
Workflow:
The original data are reads in fastq format. Some preprocessing can be done (quality trimming etc)
Reads are aligned to the genome to produce sam/bam file. This is SLOW. The file is then sorted and indexed.
Bam files can be used in the browser, but they are big. We will report only the number of reads at each position in a wig (wiggle) format.
Wig files can be loaded to the database but perhaps more efficiently converted to binary bigwig files. The database then contains only reference to bigwig file.
Data:
malGlo [8] - only reads provided. Out of 27 experiments choose only 1-2, align to genome, e.g. this one: [9]
to create track, place bigwig file to appropriate place in /gbdb
then create table with reference to this file:
hgsql malXyz1 -e "CREATE TABLE table_name (fileName varchar(255) not null);"
hgsql malXyz1 -e "insert into table_name values ('/gbdb/malXyz1/filename.bw');"
in trackDb.ra include something like this: (change 500 to appropriate value at which read depth is clipped)
track table_name
shortLabel RNA-seq coverage
longLabel RNA-seq coverage
visibility dense
group rna
type bigWig 0 500
composite track from multiple experiments:
track track_name
compositeTrack on
type bigWig 0 200
shortLabel RNA-seq coverage
longLabel RNA-seq coverage
group rna
visibility dense
track subtrack_name
shortLabel subtrack_label
longLabel subtrack_label
parent track_name
type bigWig 0 250
visibility full
maxHeightPixels 80:16:8
- Last year notes: https://github.com/fmfi-genomika/genomika-2017/wiki/Expression-tracks
- However steps there are mostly not recommended this year
- Last year tracks, see RNA-seq WT1 (L) in yarLip browser
to create track, place bigwig file to appropriate place in /gbdb
then create table with reference to this file:
hgsql malXyz1 -e "CREATE TABLE table_name (fileName varchar(255) not null);" hgsql malXyz1 -e "insert into table_name values ('/gbdb/malXyz1/filename.bw');"
in trackDb.ra include something like this: (change 500 to appropriate value at which read depth is clipped)
track table_name shortLabel RNA-seq coverage longLabel RNA-seq coverage visibility dense group rna type bigWig 0 500
composite track from multiple experiments:
track track_name compositeTrack on type bigWig 0 200 shortLabel RNA-seq coverage longLabel RNA-seq coverage group rna visibility dense
track subtrack_name shortLabel subtrack_label longLabel subtrack_label parent track_name type bigWig 0 250 visibility full maxHeightPixels 80:16:8