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SourceForge net sequence alignment map files
Sequence Alignment Map Files, supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/sequence+map/sequence+alignment+map++sam++tools/pmc07505471-79-2-6
Average 90 stars, based on 1 article reviews
sequence alignment map files - by Bioz Stars, 2026-09
90/100 stars

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Article Title: A missense mutation in Pitx2 leads to early-onset glaucoma via NRF2-YAP1 axis
Article Snippet: High-quality reads were mapped to the mouse genome (GRCm38, mm10) and the resulting alignment was sorted by coordinates and further converted to binary alignment map (BAM) format by Picard v1.95 SortSam utility ( http://picard.sourceforge.net ).

Article Title: Spectrum of genetic mutations in methylmalonic aciduria among Iranian patients
Article Snippet: Next, Sequence Alignment/Map (SAM) tools version 1.6 ( http://samtools.sourceforge.net ) were used for detection and removal of duplicates.

Article Title: Chronological set of E. coli O157:H7 bovine strains establishes a role for repeat sequences and mobile genetic elements in genome diversification.
Article Snippet: SAM files were reformatted using Sequence Alignment/Map (SAM) tools (http://samtools.sourceforge. net), and Pilon 1.22 [35] was used to identify and resolve sequence variants.

Article Title: Chronological set of E. coli O157:H7 bovine strains establishes a role for repeat sequences and mobile genetic elements in genome diversification
Article Snippet: SAM files were reformatted using Sequence Alignment/Map (SAM) tools ( http://samtools.sourceforge.net ), and Pilon 1.22 [ ] was used to identify and resolve sequence variants.

Article Title: Protein coding variation in the J:ARC and J:DO outbred laboratory mouse stocks provides a molecular basis for distinct research applications
Article Snippet: The resulting alignment was sorted by coordinates and converted to binary alignment map (BAM) format by Picard v 2.8.1- SortSam utility ( http://picard.sourceforge.net ).

Sequencing:

Article Title: Whole exome sequencing identified a pathogenic nonsense mutation in LMNA in a family with a progressive cardiac conduction defect: A case report
Article Snippet: Picard (version 1.119; sourceforge.net/projects/picard ) and Genome Analysis Toolkit (version 3.7) ( ) tools were used for duplicate removal, local realignment and base quality recalibration. .. Single nucleotide polymorphism (SNP) and Indel calling were performed using Sequence Alignment Map tools (version 1.10; samtools.sourceforge.net/ ) and were annotated using Annotate Variation (version 20170825) , according to the SNP database ( www.ncbi.nlm.nih.gov/SNP ) and the 1000 Genomes Project database ( www.1000genomes.org/index.html ). ..

Article Title: Comparative transcriptome analysis uncovers different heat stress responses in heat-resistant and heat-sensitive jujube cultivars.
Article Snippet: Cleaned RNA-seq reads were then mapped to the jujube reference genome retrieved from the NCBI Database (http://www. ncbi.nlm.nih.gov/genome/) [28] using Bowtie 2 (http://bowtie-bio.sourceforge.net/index. shtml) [29] and TopHat 2 (http://ccb.jhu.edu/software/tophat/index.shtml) [30]. .. Then the Sequence Alignment Map (http://samtools.sourceforge.net) [31] files were generated by TopHat2 and subsequently transcripts were assembled by Cufflinks (http://cufflinks.cbcb. umd.edu/) [32]. ..

Article Title: Comparative transcriptome analysis uncovers different heat stress responses in heat-resistant and heat-sensitive jujube cultivars
Article Snippet: Cleaned RNA-seq reads were then mapped to the jujube reference genome retrieved from the NCBI Database ( http://www.ncbi.nlm.nih.gov/genome/ ) [ ] using Bowtie 2 ( http://bowtie-bio.sourceforge.net/index.shtml ) [ ] and TopHat 2 ( http://ccb.jhu.edu/software/tophat/index.shtml ) [ ]. .. Then the Sequence Alignment Map ( http://samtools.sourceforge.net ) [ ] files were generated by TopHat2 and subsequently transcripts were assembled by Cufflinks ( http://cufflinks.cbcb.umd.edu/ ) [ ]. ..

Generated:

Article Title: Comparative transcriptome analysis uncovers different heat stress responses in heat-resistant and heat-sensitive jujube cultivars.
Article Snippet: Cleaned RNA-seq reads were then mapped to the jujube reference genome retrieved from the NCBI Database (http://www. ncbi.nlm.nih.gov/genome/) [28] using Bowtie 2 (http://bowtie-bio.sourceforge.net/index. shtml) [29] and TopHat 2 (http://ccb.jhu.edu/software/tophat/index.shtml) [30]. .. Then the Sequence Alignment Map (http://samtools.sourceforge.net) [31] files were generated by TopHat2 and subsequently transcripts were assembled by Cufflinks (http://cufflinks.cbcb. umd.edu/) [32]. ..

Article Title: Comparative transcriptome analysis uncovers different heat stress responses in heat-resistant and heat-sensitive jujube cultivars
Article Snippet: Cleaned RNA-seq reads were then mapped to the jujube reference genome retrieved from the NCBI Database ( http://www.ncbi.nlm.nih.gov/genome/ ) [ ] using Bowtie 2 ( http://bowtie-bio.sourceforge.net/index.shtml ) [ ] and TopHat 2 ( http://ccb.jhu.edu/software/tophat/index.shtml ) [ ]. .. Then the Sequence Alignment Map ( http://samtools.sourceforge.net ) [ ] files were generated by TopHat2 and subsequently transcripts were assembled by Cufflinks ( http://cufflinks.cbcb.umd.edu/ ) [ ]. ..



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