| 26 | | * Use [[http://tophat.cbcb.umd.edu/manual.html|TopHat]] (or another spliced mapper) to map short reads to genome of choice with default settings except |
| 27 | | * Selecting a value for --segment-length equal to half of the read length can greatly help spliced mapping (across an intron) [''ex: For 40-nt reads, use '--segment-length 20' '']. For longer reads (>~45 bases), the default value (25) can be used. |
| 28 | | * choose encoding based on the your data's [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|FastQC]] report, which is located in "Basic Statistics" -> Encoding. |
| 29 | | * --solexa-quals: Solexa/Illumina before 1.3 |
| 30 | | * --solexa1.3-quals: >= Illumina 1.3 and < Illumina 1.8 |
| 31 | | * Supplying a GTF file describing gene models to TopHat can provide better mapping of some spliced reads. |
| | 26 | * Use [[http://tophat.cbcb.umd.edu/manual.html|TopHat]] (or another spliced mapper) to map short reads to the genome of choice. |
