PALMapper statistics

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PALMapper specifications

Information


Unique identifier OMICS_01245
Name PALMapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A genome sequence, a read data to align and an optional genome annotation file, donor and acceptor splice-site predictions and a QPALMA parameter file.
Input format FASTA+FASTQ/GFF3+SPF
Operating system Unix/Linux, Mac OS
Database management system MySQL
Computer skills Advanced
Version 0.5
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Gunnar Rätsch <>

Additional information


http://www.raetschlab.org/suppl/palmapper/tutorial

Publication for PALMapper

PALMapper in publications

 (12)
PMCID: 5548721
PMID: 28790409
DOI: 10.1038/s41598-017-07866-6

[…] the rna-seq reads for all 19 magic founders as available in the gsm764077-gsm764082 and gse53197 releases for each of the three organs (seedling, root, and stage-12 floral bud) were aligned with palmapper to the arabidopsis genome for read quantification after gan et al.. the quantification of gene expression and normalization were as described previously, and normalized expression (sense […]

PMCID: 5378104
PMID: 28179367
DOI: 10.1534/genetics.116.192823

[…] lane, samples were barcoded and run in 13-plexes to give ∼14 million reads per sample., all libraries were aligned to the tair10 reference gene set augmented by any novel genes reported in using palmapper v0.6 (), following a variation-aware alignment approach. genome variants collected from the 19 founder strains, as well as variants reported for a diverse natural population () […]

PMCID: 4978887
PMID: 27226169
DOI: 10.1534/g3.116.030874

[…] fully sequenced genomes and transcriptomes () from plants grown at 10° and 16°. here, rna had been prepared from whole rosettes collected at the 9-true-leaf stage. rna reads had been aligned using palmapper aligner using a variant-aware alignment strategy. reads that were longer than 24 bp and uniquely mapped into the exonic regions had been used to quantify expression. further details […]

PMCID: 4728800
PMID: 26813401
DOI: 10.1186/s13059-016-0881-8

[…] mapped to locate exons, then unmapped reads are split and aligned independently to identify exon junctions [, ]. several other mappers exist that are optimized to identify snps or indels (gsnap [], palmapper [] mapsplice []), detect non-canonical splice junctions (star [], mapsplice []), achieve ultra-fast mapping (gem []) or map long-reads (star []). important parameters to consider […]

PMCID: 4554858
PMID: 26323406
DOI: 10.5713/ajas.15.0143

[…] novel spliced transcripts consisting of novel splicing events of known annotated exons. several programs are available for such analysis, including qpalma, splicemap, mapsplice, tophat, gsnap and palmapper, in which the tophat algorithm pairs candidate exons and evaluates the alignment of reads to such candidates (). in this study, mrna for 29,997 genes was detected including 15,518 novel […]


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PALMapper institution(s)
Friedrich Miescher Laboratory, Max Planck Society, Tübingen, Germany
PALMapper funding source(s)
Supported by the Max Planck Society, the EU under the PASCAL2 Network of Excellence (ICT-216886), and DFG Grant RA1894/1-1.

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