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Showing 1 - 25 of 33 protocols
AccessionType
 
nucleic acid sequencing protocol
Illumina 76bp paired-end reads
nucleic acid extraction protocol
Trizol
nucleic acid library construction protocol
Illumina mRNA-seq library construction protocol
growth protocol
Cells were cultured in RPMI supplemented with 10% FBS.
data generation protocol
Simulated data were generated from human genome reference GRCh37 using the BEERS toolkit (Grant et al., Bioinformatics 27: 2518–2528), additionally modeling base-call errors and quality scores with simNGS (http://www.ebi.ac.uk/goldman-srv/simNGS). Gene models were based on GENCODE annotation and several additional gene catalogs. Novel transcript isoforms were simulated to emulate a realistic scenario where gene annotation is incomplete. Retained introns were also included to reflect a proportion of pre-spliced mRNAs captured by RNA-seq. Substitution variants were introduced into exons at rates of 0.001 (simulation 1) and 0.0005 (simulation 2) events per bp, and indel polymorphisms at rates of 0.0005 (simulation 1) and 0.0025 (simulation 2). The proportion of signal originating from novel simulated transcript isoforms was 20% and 35% for simulations 1 and 2, respectively. The program simNGS recreates observations from Illumina sequencing machines using the statistical models underlying the AYB base-calling software (Massingham and Goldman, Genome Biol. 13: R13). To simulate base-call errors and quality scores, simNGS version 1.5 was applied using a paired-end simulation model. The model was trained on intensity data released by Illumina from a sequencing run on the HiSeq 2000 instrument with TruSeq chemistry. Simulation files are provided here: http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-1728/simulated_transcriptomes.tar.gz
high throughput sequence alignment protocol
PALMapper with filtering, score optimization and annotation
high throughput sequence alignment protocol
PALMapper with filtering and score optimization
high throughput sequence alignment protocol
PALMapper with multimapper resolution and annotation
high throughput sequence alignment protocol
PALMapper with multimapper resolution
high throughput sequence alignment protocol
MapSplice with annotation
high throughput sequence alignment protocol
GEM with de novo junction discovery and annotation
high throughput sequence alignment protocol
STAR 1-pass
high throughput sequence alignment protocol
ReadsMap
high throughput sequence alignment protocol
SMALT
high throughput sequence alignment protocol
PASS
high throughput sequence alignment protocol
PASS with coverage filter
high throughput sequence alignment protocol
TopHat version 1.3.2
high throughput sequence alignment protocol
STAR 2-pass with annotation
high throughput sequence alignment protocol
TopHat version 2.0.3
high throughput sequence alignment protocol
TopHat version 1.3.2 with annotation
high throughput sequence alignment protocol
STAR 2-pass
high throughput sequence alignment protocol
STAR 1-pass with annotation
high throughput sequence alignment protocol
BAGET pipeline, using annotation
high throughput sequence alignment protocol
GEM with conservative de novo junction discovery