SAMStat statistics

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Associated diseases

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SAMStat specifications

Information


Unique identifier OMICS_01073
Name SAMStat
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FASRQ, BAM, SAM
Output data A single html5 page containing several plots.
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.5.1
Stability Beta
Maintained Yes

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Publication for SAMStat

SAMStat in publications

 (25)
PMCID: 5883058
PMID: 29615708
DOI: 10.1038/s41598-018-23802-8

[…] reads obtained after the trimming were aligned against the a. carbonarius v3 reference genome (http://genome.jgi.doe.gov/aspca3/aspca3.home.html). to check the mapping quality of the alignment, samstat software was used. the resulting alignment file was pre-processed to make it adequate for variant calling analysis. the reads with a mapping quality less than 30 were removed using samtools […]

PMCID: 5857375
PMID: 29319470
DOI: 10.1099/mgen.0.000148

[…] using the bwa software []. the maximum number of mismatches was four, the seed length was 32 and two mismatches were allowed within the seed. files in bam format were processed with the samstat (version 1.08) software (http://samstat.sourceforge.net/) to confirm sequence quality and for mapping statistics. each sample yielded between 2 and 4 million reads. bedtools (version 2.21.0) […]

PMCID: 5785776
PMID: 29499940
DOI: 10.1016/j.omtn.2017.12.008

[…] gencode.v23.primary_assembly.annotation.gff3–sjdboverhang 100–sjdbgtftagexonparenttranscript parent). the alignment step, the post-processing of reads with samstat 1.5 and bedtools 2.17.0, and the read count per gene with htseq 0.6.1 were automatized with a dedicated bash script available at […]

PMCID: 5687707
PMID: 29140992
DOI: 10.1371/journal.pone.0187735

[…] genome sequence set sus scrofa 10.2 [] was performed with tophat [], which is an efficient read-mapping algorithm designed to align reads and makes substantial use of the tool bowtie 2 [,]. the samstat program [] was used to display all statistics for mapped and unmapped reads. the toolset bedtools [] and gene information from entrez gene id [] were used to display an expression table […]

PMCID: 5686165
PMID: 29138416
DOI: 10.1038/s41598-017-15481-8

[…] reads were mapped on tomato genome using the spliced transcripts alignment to a reference (star) software. statistics for unmapped, poorly and accurately mapped reads were obtained using samstat software. reads count was performed by using featurecounts. differentially expressed genes (degs) were identified and clustered according to expression profiles using the ‘edger’ package […]


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SAMStat institution(s)
Omics Science Center, Riken Yokohama Institute, Tsurumi-ku, Yokohama, Japan
SAMStat funding source(s)
Supported by Research Grant for the RIKEN Omics Science Center from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government (MEXT).

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