General information on the multiple input and output file formats processed by SeqCode.

SeqCode defines the content of the genome from one file containing the name and the size of the chromosomes of the organism. The UCSC genome browser provides this information through the Downloads section for each genome (Annotation database link). Thus, users can retrieve the corresponding chromInfo.txt file for the appropriate organism. For example, the mouse file (mm9) is accessible from http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz. These files must be uncompressed previously to be used with SeqCode and the name of alternative contigs (e.g. chr13_random) can be dismissed into the final archive.

This is an example of this class of files for mouse (genome assembly: mm9):

chr1    197195432
chr10   129993255
chr11   121843856
chr12   121257530
chr13   120284312
chr14   125194864
chr15   103494974
chr16   98319150
chr17   95272651
chr18   90772031
chr19   61342430
chr2    181748087
chr3    159599783
chr4    155630120
chr5    152537259
chr6    149517037
chr7    152524553
chr8    131738871
chr9    124076172
chrM    16299
chrX    166650296
chrY    15902555 

SeqCode uses the gene transcript annotations provided by the RefSeq consortium to define the location of genomic features on virtually any genome that is served by this project. The UCSC genome browser provides this information through the Downloads section for each genome (Annotation database link). Thus, users can retrieve the corresponding refGene.txt.gz file for the appropriate organism. For example, the mouse file (mm9) is accessible from http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/refGene.txt.gz. Such files must be uncompressed previously to be used with SeqCode (e.g. gzip -d refGene.txt.gz).

This is an extract of the refGene.txt file for mouse (genome assembly: mm9), each line contains the information for a RefSeq transcript:

This is the description of each field in this class of files according to the UCSC table browser:

SeqCode mainly analyzes the set of mapped reads of a sequencing experiment (e.g. ChIPseq/RNAseq/ATACseq) in SAM format. This file format contains one line per read that is mapped, containing the location in the genome for such a read. BAM files, which are the compressed version of SAM files, can be also provided to SeqCode. For further information, users can access the SAM format documentation at https://samtools.github.io/hts-specs/SAMv1.pdf.

This is an extract of a SAM file from the mapping of a ChIPseq experiment:



Implementation notes (SeqCode requirements):
- SAM/BAM files should exclusively contain aligned reads (unmapped reads with flag=4 must be removed).
- SAM/BAM file indexing and sorting is not required to perform SeqCode analyses.

The location of ChIPseq peaks or any other genomic feature can be easily represented using the BED format (Browser Extensible Data, see the UCSC documentation for further information). In the simplest version of this format, each line in these files contains 4 columns: chromosome, initial position, ending position and (optionally) a name for identifying this element.

This is an example of a BED format file:

chr1    4481268 4484041 MACS_peak_1
chr1    4485405 4487849 MACS_peak_2
chr1    5008529 5011367 MACS_peak_3
chr1    9788194 9789005 MACS_peak_4
chr1    9838297 9839446 MACS_peak_5
(...)

SeqCode generates custom tracks for visualization in genome browsers using the BedGraph format. With this format, it is possible to produce distribution functions to map the location of high-throughput experiments or other features along the chromosomes (more information on the UCSC genome browser documentation). Basically, it is derived from the BED format by adding a number in the 4th column to define the height of the profile in that region.

This is an excerpt of this type of files:

track type=bedGraph name="NAME" description="TEXT" visibility="full" color="0,0,100"
chr1    2999917 3000116 1
chr1    3000117 3000241 1
chr1    3001026 3001226 1
chr1    3001269 3001468 1
chr1    3001469 3001580 1
chr1    3002287 3002486 1
chr1    3002487 3002566 1
chr1    3002567 3002735 2
chr1    3002736 3002767 1
chr1    3003804 3004004 1
(...)

To calculate the conservation of a genomic region, SeqCode uses the PhastCons data files provided by the UCSC genome browser. These files provide chromosome by chromosome the scores of the multiple comparison between the reference species and a group of other genomes. For instance, the folder http://hgdownload.soe.ucsc.edu/goldenPath/mm9/phastCons30way/ provides the data files for the phastCons30way track in which mouse is compared to 30 vertebrates. Please, note that such files must be uncompressed previously to be used with SeqCode (estimated average size per mouse chromosome around 1 GigaByte).

This is an excerpt of this type of files for mouse (genome assembly: mm9):

fixedStep chrom=chr1 start=3000306 step=1
0.006
0.010
0.014
0.017
0.019
0.021
0.021
0.021
0.019
(...)