User talk:Darek Kedra/sandbox 29: Difference between revisions
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=== SNPs discovery === | === SNPs discovery === | ||
* [https://www.broadinstitute.org/gatk/ GATK] ver 3.2-2 | * [https://www.broadinstitute.org/gatk/ GATK] ver 3.2-2 | ||
==01 Data files used == | |||
===FASTQ files === | |||
====L.amazonensis RNA-Seq ==== | |||
* http://www.ebi.ac.uk/ena/data/view/SRP016502 | |||
====L mexicana genomic DNA === | |||
* http://www.ebi.ac.uk/ena/data/view/ERX280624 | |||
==== (extra set) L.enriettii genomic DNA ==== | |||
* http://www.ebi.ac.uk/ena/data/view/SRR835620 | |||
==NGS file formats== | ==NGS file formats== | ||
Revision as of 09:35, 11 September 2014
EMBO Tunis 2014
From sequencing data to knowledge
00 Programs used
sequence pre-processing
- SRA_toolkit ver current
- FastQC ver 0.11.2
- Trimmomatic ver 0.32
- TagDust ver 2.13
- Coral ver 1.4
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
quantification
SNPs discovery
- GATK ver 3.2-2
01 Data files used
FASTQ files
L.amazonensis RNA-Seq
=L mexicana genomic DNA
(extra set) L.enriettii genomic DNA
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)
