User talk:Darek Kedra/sandbox 29: Difference between revisions
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* [http://www.well.ox.ac.uk/~gerton/software/Stampy/ Stampy] stampy-1.0.23r2059.tgz (optional) | * [http://www.well.ox.ac.uk/~gerton/software/Stampy/ Stampy] stampy-1.0.23r2059.tgz (optional) | ||
=== Splice reader mappings === | |||
* [https://github.com/indraniel/fqgrep fqgrep] Github version plus | |||
* [https://github.com/laurikari/tre/ TRE_library] ver 0.80 | |||
=== viewers=== | |||
* [http://www.broadinstitute.org/igv/home IGV] ver 2.3.34 | |||
* [ http://www.broadinstitute.org/igv/download igvtools] ver 2.3.32 | |||
=== quantification === | === quantification === | ||
Revision as of 08:52, 9 September 2014
EMBO Tunis 2014
From sequencing data to knowledge
00 Programs used
sequence pre-processing
- FastQC ver 0.11.2
- Trimmomatic ver 0.32
- TagDust ver 2.13
general tools
- fastx_toolkit ver 0.0.13
- Samtools classic ver 0.1.19
- samtools/HTSlib ver 1.0
- Picard ver 1.119
mappers
Splice reader mappings
- fqgrep Github version plus
- TRE_library ver 0.80
viewers
- IGV ver 2.3.34
- [ http://www.broadinstitute.org/igv/download igvtools] ver 2.3.32
quantification
SNPs discovery
- GATK ver 3.2-2
NGS file formats
- FASTQ
- SAM
- BAM,
- VCF,
- GTF/GFF
- BED
pre-processing FASTQ files =
Mapping Illumina reads with LAST (possibly also with BWA/Stampy: check with G.Benson)
Quick and dirty genome 2 genome comparison using LAST
- Comparing 2-3 Leishmania genomes
Viewing mapping results with IGV
SNP discovery (GATK)
Quantifications of mapped reads
- Gene quantifications (DNA & RNA levels)
