User talk:Darek Kedra/sandbox 29: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
Darek Kedra (talk | contribs) |
Darek Kedra (talk | contribs) |
||
| Line 41: | Line 41: | ||
* http://www.ebi.ac.uk/ena/data/view/SRP016502 | * http://www.ebi.ac.uk/ena/data/view/SRP016502 | ||
====L mexicana genomic DNA === | ====L mexicana genomic DNA ==== | ||
* http://www.ebi.ac.uk/ena/data/view/ERX280624 | * http://www.ebi.ac.uk/ena/data/view/ERX280624 | ||
Revision as of 09:36, 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)
