https://sourceforge.net/p/tuque/wiki/FileFormats/Recent changes to FileFormatsenWed, 10 Apr 2013 17:20:51 -0000https://sourceforge.net/p/tuque/wiki/FileFormats/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -1,17 +1,16 @@ File formats ============ -The input RNA-Seq reads should be in Fastq format [http://maq.sourceforge.net/fastq.shtml]. tuqueSplice and tuqueMap -determine the read length and quality value encoding automatically; these values should be constant within each reads file, but can differ between input files. +The input RNA-Seq reads should be in __Fastq__ format \[l\]. tuqueSplice and tuqueMap determine the read length and quality value encoding automatically; these values should be constant within each reads file, but can differ between input files. -The genome sequence file should contain the sequence of each chromosome (or scaffold or contig) in Fasta format -[http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml]. +The genome sequence file should contain the sequence of each chromosome (or scaffold or contig) in __Fasta__ format +\[\]. -Sequence feature annotations should be in GFF3 format [http://www.sequenceontology.org/gff3.shtml]. +Sequence feature annotations should be in __GFF3__ format \[\]. -Read mappings are output in BAM format [http://samtools.sourceforge.net/SAM1.pdf]. +Read mappings are output in __BAM__ format \[\]. -The .juncs format is as used in early versions of Tophat. +The __.juncs__ format is as used in early versions of Tophat. It is a tab-delimited text format, with one line for each splice junction. Each line contains at least 4 fields separated by tab characters: 1. Chromosome Id @@ -28,4 +27,4 @@ 10. Right anchor - the maximum distance between the junction and the 3' end of a spanning read 11. Class - either regular, variant, or wrongway. -The coverage.wig files are in bedGraph format [http://genome.ucsc.edu/goldenPath/help/bedgraph.html] +The coverage.wig files are in __bedGraph__ format \[\] </pre> </div>Ian ReidWed, 10 Apr 2013 17:20:51 -0000https://sourceforge.netdf0f1c721c268eacbadbf3a26bf81c4a99aa6b92https://sourceforge.net/p/tuque/wiki/FileFormats/<div class="markdown_content"><h1 id="file-formats">File formats</h1> <p>The input RNA-Seq reads should be in Fastq format <span>[http://maq.sourceforge.net/fastq.shtml]</span>. tuqueSplice and tuqueMap<br /> determine the read length and quality value encoding automatically; these values should be constant within each reads file, but can differ between input files.</p> <p>The genome sequence file should contain the sequence of each chromosome (or scaffold or contig) in Fasta format<br /> <span>[http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml]</span>.</p> <p>Sequence feature annotations should be in GFF3 format <span>[http://www.sequenceontology.org/gff3.shtml]</span>.</p> <p>Read mappings are output in BAM format <span>[http://samtools.sourceforge.net/SAM1.pdf]</span>.</p> <p>The .juncs format is as used in early versions of Tophat.<br /> It is a tab-delimited text format, with one line for each splice junction. Each line contains at least 4 fields<br /> separated by tab characters:<br /> 1. Chromosome Id<br /> 2. Start - the 0-based genomic coordinate of the first base that is spliced out<br /> 3. End - the 0-based genomic coordinate of the last base that is spliced out<br /> 4. Strand - either + or -</p> <p>.juncs files produced by tuqueSplice contain additional fields:<br /> 5. Read-through ratio - the ratio of the mean read coverage depth on the spliced-out bases to the coverage depth on the bases immediately before and immediately after the junction<br /> 6. Multiplicity - the number of mapped reads that are spliced at this junction<br /> 7. Diversity - the number of distinct reads that are spliced at this junction<br /> 8. Donor-acceptor pair of the spliced-out intron<br /> 9. Left anchor - the maximum distance between the 5' end of a spanning read and the junction<br /> 10. Right anchor - the maximum distance between the junction and the 3' end of a spanning read<br /> 11. Class - either regular, variant, or wrongway.</p> <p>The coverage.wig files are in bedGraph format <span>[http://genome.ucsc.edu/goldenPath/help/bedgraph.html]</span></p></div>Ian ReidWed, 10 Apr 2013 17:05:25 -0000https://sourceforge.neta7b6a3dac342d835e14215b772c64d4f48d53198