HUMAN DEVELOPMENTAL BIOLOGY, 
University of Manchester, UK.


This folder contains files produced by mapping sequence data to the human genome (Version: hg19).


# SAMPLES --------------------------------------


Filenames begin with the name of the sample. e.g. Liver_2topHat_hg19_.unique.bed12.gz is from sample Liver_2

# ANALYSES ---------------------------------

The analysis (e.g. mapping) pipeline is denoted by the central section of the filename.

e.g. *topHat_hg19_.unique*  is a dataset resulting from mapping to the human genome (hg19) using TopHat and retaining uniquely mapped reads.
# TODO list pipelnies in another directory.


# FILE-TYPES -------------------------------------


The different file name endings are for different types of files:-

*.bw 	A UCSC BigWig file. This binary file is accessed remotely when using the UCSC track hub to view data.

	*.FIRST.bw   A bigwig file showing only reads mapped to the chromosomal first strand ('+' / Watson). In the track hub viewed in Green.	
	*.SECOND.bw   A bigwig file showing only reads mapped to the chromosomal second strand ('-' / Crick). In the track hub viewed in Blue.


*.bb	A binary BigBed file (see https://genome.ucsc.edu/FAQ/FAQformat.html#format1.5) giving the location of features on the genome. Like *.bw, bigbed files are hosted here to be viewed by the UCSC track hub.

e.g. multiTissue.novel.transcripts.2015.6251.bb     6251 novel transcripts 

	
*.bed12.gz   A 'bed' format plain text file (gzip compressed) listing the position of mapped reads (one line per mapping). 'bed12' includes columns detailing the 	

example unspliced reads: -
chr1    13442   13543   D3YGT8Q1:262:C5T4HACXX:5:1213:12286:32070/1     50      -       13442   13543   255,0,0 1       101     0
chr1    13442   13543   D3YGT8Q1:263:C5R1AACXX:8:1107:20580:76414/1     50      -       13442   13543   255,0,0 1       101     0
chr1    14460   14561   D3YGT8Q1:263:C5R1AACXX:8:2302:9789:73113/1      50      -       14460   14561   255,0,0 1       101     0
chr1    14466   14567   D3YGT8Q1:263:C5R1AACXX:7:2307:9874:91923/1      50      -       14466   14567   255,0,0 1       101     0
chr1    14471   14572   D3YGT8Q1:262:C5T4HACXX:5:1212:14921:89361/1     50      -       14471   14572   255,0,0 1       101     0
chr1    14488   14589   D3YGT8Q1:262:C5T4HACXX:5:1315:6889:30695/1      50      -       14488   14589   255,0,0 1       101     0

columns are: chr, start, end, sequence name (from sequencing machine), topHat mapping quality (always 50 for uniquely mapped reads), strand, start, end, colour, blockCount, blockSizes, blockStarts
(see https://genome.ucsc.edu/FAQ/FAQformat.html#format1)

For the RNA-seq, read-pairs can be reconstructed from the sequence names. The two names end /1 and /2, respectively.

example spliced reads:-
chr1    787408  788069  D3YGT8Q1:263:C5R1AACXX:7:1213:3733:45416/2      50      +       787408  788069  255,0,0 2       82,19   0,642
chr1    787412  788073  D3YGT8Q1:262:C5T4HACXX:5:1109:13655:86089/2     50      +       787412  788073  255,0,0 2       78,23   0,638
chr1    787412  788073  D3YGT8Q1:262:C5T4HACXX:5:2103:14380:95672/2     50      +       787412  788073  255,0,0 2       78,23   0,638
chr1    787412  788073  D3YGT8Q1:263:C5R1AACXX:7:1209:10060:75058/2     50      +       787412  788073  255,0,0 2       78,23   0,638
chr1    787412  788073  D3YGT8Q1:263:C5R1AACXX:8:1212:9382:61309/2      50      +       787412  788073  255,0,0 2       78,23   0,638
chr1    787413  788074  D3YGT8Q1:262:C5T4HACXX:5:1215:11377:24343/2     50      +       787413  788074  255,0,0 2       77,24   0,637
chr1    787449  788110  D3YGT8Q1:262:C5T4HACXX:5:2113:4547:20426/2      50      +       787449  788110  255,0,0 2       41,60   0,601
chr1    787449  788110  D3YGT8Q1:263:C5R1AACXX:7:2210:11746:69521/2     50      +       787449  788110  255,0,0 2       41,60   0,601

Note that the last three columns give the precise locations of splicing events relative to the start (column 3) (see https://genome.ucsc.edu/FAQ/FAQformat.html#format1).



DOWNLOADs

Be sure to check the files have downloaded correctly by checking the md5sum values on your own machine
Our md5sum values are in ./bed12.gz.md5sum


For further project and sample information contact Prof. Neil Hanley (neil.hanley@manchester.ac.uk)
For data queries, contact Dr Dave Gerrard (david.gerrard@manchester.ac.uk)