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SourceForge net samtools software package
Samtools Software Package, 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/samtools/samtools+software/pmc04630673-274-1-5
Average 90 stars, based on 1 article reviews
samtools software package - by Bioz Stars, 2026-11
90/100 stars

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Related Articles

Polymerase Chain Reaction:

Article Title: Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in Aegilops tauschii
Article Snippet: .. Duplicate reads resulting from PCR amplification were removed using the markdup function in the Samtools software ( https://sourceforge.net/projects/samtools/ , accessed on 17 April 2023) [ ]. ..

Amplification:

Article Title: Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in Aegilops tauschii
Article Snippet: .. Duplicate reads resulting from PCR amplification were removed using the markdup function in the Samtools software ( https://sourceforge.net/projects/samtools/ , accessed on 17 April 2023) [ ]. ..

Software:

Article Title: Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in Aegilops tauschii
Article Snippet: .. Duplicate reads resulting from PCR amplification were removed using the markdup function in the Samtools software ( https://sourceforge.net/projects/samtools/ , accessed on 17 April 2023) [ ]. ..

Article Title: Remodeling of maternal mRNA through poly(A) tail orchestrates human oocyte-to-embryo transition.
Article Snippet: .. Then, the files were filtered by samtools software (http://samtools.sourceforge.net, version 1.9) with the following parameters ‘-F 3844 -bS’ (https://broadinstitute.github. io/picard/explain-flags.html). ..

Article Title: The effects of length and sequence of gRNA on Cas13b and Cas13d activity in vitro and in vivo.
Article Snippet: .. Samtools software (version 1.9, https://sourceforge.net/projects/samtools/files/samtools/1.9/; parameters : -b -S -h) was used to transform Sam files into BAM files and sort them. .. After sorting, The featureCounts program in the subread package (version 2.0.1, http://subread.sourceforge.net/; parameters: -t exon -g gene_id, ) was used for gene level quantification.

Article Title: Characterization of feed efficiency-related key signatures molecular in different cattle breeds.
Article Snippet: .. The sam files were converted to the bam files using samtools software [25] (version 1.9, https:// sourceforge.net/projects/samtools/files/samtools/1.9/; parameters: -b -S -h), and the bam file https://doi.org/10.1371/journal.pone.0289939.g001 PLOS ONE | https://doi.org/10.1371/journal.pone.0289939 September 27, 2023 3 / 19 index was constructed, following gene quantification using the featureCounts program in the subread package [26] (version 2.0.1, http://subread.sourceforge.net/; parameters: -t exon -g gene_id) to acquire the count matrix, and the TPM value (Transcripts Per Kilobase of exon model per Million mapped reads) was selected to show the level of gene expression. ..

Article Title: Multi-transcriptomics reveals RLMF axis-mediated signaling molecules associated with bovine feed efficiency
Article Snippet: .. The sam files were converted to the bam files using samtools software ( ) (version 1.9, https://sourceforge.net/projects/samtools/files/samtools/1.9/ ; parameters : -b -S -h) and the bam file index was constructed, following gene quantification using the featureCounts program in the subread package ( ) (version 2.0.1, http://subread.sourceforge.net/ ; parameters : -t exon -g gene_id ) to acquire the count matrix. ..

Article Title: Long-term exposure to diesel exhaust particles induces concordant changes in DNA methylation and transcriptome in human adenocarcinoma alveolar basal epithelial cells
Article Snippet: STAR aligner [ ] was used with the Ensembl_Homo_sapiens.GRCh37 reference genome to align the filtered reads and generate alignment files (bam files). .. Alignment metrics for the bam files were evaluated using the Samtools software (v.1.3.1) ( http://samtools.sourceforge.net ), and the results were included into Additional file : List 1. ..

Article Title: The B-type cyclin Clb4 prevents meiosis I sister centromere separation in budding yeast.
Article Snippet: The Burrow-Wheeler Aligner (bio-bwa.sourceforge.net) was used to map DNA sequences to the S. cerevisiae reference genome r64, downloaded from Saccharomyces Genome Database (www.yeastgenome.org). .. The resulting SAM (Sequence Alignment/Map) file was converted to a BAM file, an indexed pileup format file, using the samtools software package (samtools.sourceforge.net). .. GATK (gatk.broadinstitute.org/hc/en-us) was used to realign local indels, and Varscan (varscan.sourceforge.net) was used to call variants.

Article Title: Characterization of feed efficiency-related key signatures molecular in different cattle breeds
Article Snippet: .. The sam files were converted to the bam files using samtools software [ ] (version 1.9, https://sourceforge.net/projects/samtools/files/samtools/1.9/ ; parameters : -b -S -h), and the bam file index was constructed, following gene quantification using the featureCounts program in the subread package [ ] (version 2.0.1, http://subread.sourceforge.net/ ; parameters : -t exon -g gene_id) to acquire the count matrix, and the TPM value (Transcripts Per Kilobase of exon model per Million mapped reads) was selected to show the level of gene expression. ..

Construct:

Article Title: Characterization of feed efficiency-related key signatures molecular in different cattle breeds.
Article Snippet: .. The sam files were converted to the bam files using samtools software [25] (version 1.9, https:// sourceforge.net/projects/samtools/files/samtools/1.9/; parameters: -b -S -h), and the bam file https://doi.org/10.1371/journal.pone.0289939.g001 PLOS ONE | https://doi.org/10.1371/journal.pone.0289939 September 27, 2023 3 / 19 index was constructed, following gene quantification using the featureCounts program in the subread package [26] (version 2.0.1, http://subread.sourceforge.net/; parameters: -t exon -g gene_id) to acquire the count matrix, and the TPM value (Transcripts Per Kilobase of exon model per Million mapped reads) was selected to show the level of gene expression. ..

Article Title: Multi-transcriptomics reveals RLMF axis-mediated signaling molecules associated with bovine feed efficiency
Article Snippet: .. The sam files were converted to the bam files using samtools software ( ) (version 1.9, https://sourceforge.net/projects/samtools/files/samtools/1.9/ ; parameters : -b -S -h) and the bam file index was constructed, following gene quantification using the featureCounts program in the subread package ( ) (version 2.0.1, http://subread.sourceforge.net/ ; parameters : -t exon -g gene_id ) to acquire the count matrix. ..

Article Title: Characterization of feed efficiency-related key signatures molecular in different cattle breeds
Article Snippet: .. The sam files were converted to the bam files using samtools software [ ] (version 1.9, https://sourceforge.net/projects/samtools/files/samtools/1.9/ ; parameters : -b -S -h), and the bam file index was constructed, following gene quantification using the featureCounts program in the subread package [ ] (version 2.0.1, http://subread.sourceforge.net/ ; parameters : -t exon -g gene_id) to acquire the count matrix, and the TPM value (Transcripts Per Kilobase of exon model per Million mapped reads) was selected to show the level of gene expression. ..

Gene Expression:

Article Title: Characterization of feed efficiency-related key signatures molecular in different cattle breeds.
Article Snippet: .. The sam files were converted to the bam files using samtools software [25] (version 1.9, https:// sourceforge.net/projects/samtools/files/samtools/1.9/; parameters: -b -S -h), and the bam file https://doi.org/10.1371/journal.pone.0289939.g001 PLOS ONE | https://doi.org/10.1371/journal.pone.0289939 September 27, 2023 3 / 19 index was constructed, following gene quantification using the featureCounts program in the subread package [26] (version 2.0.1, http://subread.sourceforge.net/; parameters: -t exon -g gene_id) to acquire the count matrix, and the TPM value (Transcripts Per Kilobase of exon model per Million mapped reads) was selected to show the level of gene expression. ..

Article Title: Characterization of feed efficiency-related key signatures molecular in different cattle breeds
Article Snippet: .. The sam files were converted to the bam files using samtools software [ ] (version 1.9, https://sourceforge.net/projects/samtools/files/samtools/1.9/ ; parameters : -b -S -h), and the bam file index was constructed, following gene quantification using the featureCounts program in the subread package [ ] (version 2.0.1, http://subread.sourceforge.net/ ; parameters : -t exon -g gene_id) to acquire the count matrix, and the TPM value (Transcripts Per Kilobase of exon model per Million mapped reads) was selected to show the level of gene expression. ..

Sequencing:

Article Title: The B-type cyclin Clb4 prevents meiosis I sister centromere separation in budding yeast.
Article Snippet: The Burrow-Wheeler Aligner (bio-bwa.sourceforge.net) was used to map DNA sequences to the S. cerevisiae reference genome r64, downloaded from Saccharomyces Genome Database (www.yeastgenome.org). .. The resulting SAM (Sequence Alignment/Map) file was converted to a BAM file, an indexed pileup format file, using the samtools software package (samtools.sourceforge.net). .. GATK (gatk.broadinstitute.org/hc/en-us) was used to realign local indels, and Varscan (varscan.sourceforge.net) was used to call variants.



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