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UCSC Genome Browser

Kinds of data you can show

  • BED files BED format
  • bedGraph
  • data that has chrom/start/stop. Can have a score.

BED 3:

chr1  100  500
chr1  150  300
chr1  800  1000

BED 4:

chr1  100  500   A
chr1  150  300   B
chr1  800  1000  C

BED 4 with track lines:

track name="example track, dense" color="128,0,0" visibility=dense
chr1  100  500   A
chr1  150  300   B
chr1  800  1000  C


track name="example track, pack" color="0,255,0" visibility=pack
chr1  100  500   A
chr1  150  300   B
chr1  800  1000  C

track name="example track, squish" color="200,0,200," visibility=squish
chr1  100  500   A
chr1  150  300   B
chr1  800  1000  C

track name="example track, with score" visibility=pack useScore=1
chr1  100  500   A  1000
chr1  150  300   B  500
chr1  800  1000  C  100

track name="example track, with strand" visibility=pack

chr1  100  500   A  0  -
chr1  150  300   B  0  -
chr1  800  1000  C  0  +

bedGraph. Note track line with type=bedGraph, which is important:

track type=bedGraph name="bedGraph example"
chr19 49302000 49302300 -1.0
chr19 49302300 49302600 -0.75
chr19 49302600 49302900 -0.50
chr19 49302900 49303200 -0.25
chr19 49303200 49303500 0.0
chr19 49303500 49303800 0.25
chr19 49303800 49304100 0.50
chr19 49304100 49304400 0.75
chr19 49304400 49304700 1.00

colored example:

track type=bedGraph name="bedgraph with color" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
chr19 49302000 49302300 -1.0
chr19 49302300 49302600 -0.75
chr19 49302600 49302900 -0.50
chr19 49302900 49303200 -0.25
chr19 49303200 49303500 0.0
chr19 49303500 49303800 0.25
chr19 49303800 49304100 0.50
chr19 49304100 49304400 0.75
chr19 49304400 49304700 1.00

Kinds of data you can't show

Raw reads (i.e. fastq). They need to be mapped first

Mapped reads. Visible, but they are hard to look at. They need to be aggregated and usually scaled. BAM cannot be uploaded directly, but must instead be hosted somewhere. http://helix.nih.gov/~dalerr/ex1.bam (this is hg19).

Data that are not in chrom-start-stop format, e.g.:

Genes    Thy1
Lypla1   1.21377
Tcea1    0
Atp6v1h  2.77439
Oprk1    0
Rb1cc1   2.96399
Fam150a  0
St18     0.721644
Pcmtd1   3.34769
...
...

Things you can do with UCSC

BLAT

Good hit example: TAGATTGTCTTTCGCTCTGA

Multi-hit example: ATGCACACACCACAAACACA

Multiple sequences example:

>LNA-AsBGL3
CGATCTCTGCTCTTAA
>gRNA2
CCAACACTATTAGATGTTC
>gRNA3
TAGATTGTCTTTCGCTCTGA
>gRNA_LDB1
TGGCAACTTTGACTATATGC
>HbG1_3UTR_F
atgcacacaccacaaacaca
>BGL3_TSS
ctaggctttttatagtttggggt

In-silco PCR

Forward: GTGCATATTCTGAAACGGTAGTGACT Reverse: TGCCTGGCTCCATCATATCA

Track search

Sometimes what you need is only in a different assembly!

Track hubs

Track hubs are sets of tracks that have been prepared by other people. Some are public, some only work if you have the URL.

https://helix.nih.gov/~dalerr/adean/xiang-eto2/xiang-eto2.hub.txt

Caveats

What is the y-axis? Rarely is it described. It may take reverse-engineering the analysis to figure it out. See the genomics section for an example of trying to figure out what the scores in a BED file are for a published data set.

Example data

Erythroid long noncoding RNA from Alvarez-Dominquez et al 2014, mm9. DOI: 10.1182/blood-2013-10-530683. Table S2.

Excel spreadsheet, separate worksheets for each class of ncRNA, mm9. Format:

Name         Coordinates (mm9)
lincRNA-EC1  chr5[+]23356389-23365750
lincRNA-EC2  chr18[+]54581940-54621217
lincRNA-EC3  chr4[-]109074924-109080172
...
...

Strategy: our goal is to convert:

lincRNA-EC1  chr5[+]23356389-23365750

into:

chr5    23356389   23365750   lincRNA-EC1  0   +

Physical domains from Sexton et al 2012, in fly embryro (dm3). PMID: 22265598. Table S1

Excel spreadsheet, one worksheet. Format:

Table S1: List of physical domains, related to Figure 3

domain id   chrom   start   end     epigenetic class
1   chr2L   67150   156849  Active
2   chr2L   156850  250149  Null
3   chr2L   250150  295749  Active
4   chr2L   295750  421449  HP1 centromeric
5   chr2L   421450  472049  HP1 centromeric
6   chr2L   472050  488649  Active
7   chr2L   488650  542149  PcG
8   chr2L   542150  809749  PcG
...
...

GAF ChIP-seq: GSE40646. Called peaks and WIG files. dm3.

Transcription in adult germline stem cells, PMID: 24835570.

FPKM, keyed by gene symbol. Format, for each sample:

Genes    Thy1
Lypla1   1.21377
Tcea1    0
Atp6v1h  2.77439
Oprk1    0
Rb1cc1   2.96399
Fam150a  0
St18     0.721644
Pcmtd1   3.34769
...
...