samtools --version samtools 1.18 Using htslib 1.18 Please describe your environment. OS (rununame -sron Linux/Mac OS orwmic os get Caption, Versionon Windows) uname -sr Linux 3.10.0-1160.el7.x86_64 machine architecture (rununame -mon Linux/Mac OS orwmic os get OSArchitectureon Windows) ...
Single cell chromatin accessibility profiling and transcriptome sequencing are the most widely used technologies for single-cell genomics. Here, we present Microwell-seq3, a high-throughput and facile platform for high-sensitivity single-nucleus chromatin accessibility or full-length transcriptome profiling....
38. were obtained, sorted by read name with samtools66 sort (v. 1.16.1; option -n) and converted to fastq files with samtools fastq (options -T CB --barcode-tag CB) to transcribe the barcodes to the fastq headers from the BAM headers for alignment to the hg38 reference genome, as ...
mitoABEMutH-enabled adenine editing occurred preferentially on the top strands of the three target loci (MT-ND1, MT-ND4 and MT-RNR2) (Fig. 1b and Extended Data Fig. 1c,d). Despite the presence of multiple adjacent Ts next to the edited A within the editing windows, the A on its op...
Are you using the latest version of samtools and HTSlib? If not, please specify. (run samtools --version) Please describe your environment. OS (run uname -sr on Linux/Mac OS or wmic os get Caption, Version on Windows) machine architecture (run uname -m on Linux/Mac OS or wmic os ...
Because WhatsHap calculates haplotypes only for pri- mary alignment, the phased SNPs on the supplementary alignment reads sup- porting these SV were manually counted using the SAMtools (version 1.7) mpileup function. Then, we extracted the reads with ≥2 SNPs and a ratio of the number of SNPs...
Process and Manage BAM Files: Convert SAM files to BAM format, sort, and index BAM files using Samtools, ensuring efficient data management and analysis. Filter Reads by Mapping Quality: Filter sequencing reads based on mapping quality to retain high-quality data for downstream analysis. ...
To obtain quality metrics of our duplex base called reads, we used Qualimap v2.2.2 to provide a summary report on these reads aligned to the expected reference sequence. We used minimap2 v2.17 with the “-ax map-ont --cs" options to generate a sam file, used samtools v1.7 to convert...
Subsequently, BWA [28, 29] and Samtools [30] were used with default parameters to obtain the aligned BAM file for CNV detection. In this study, we used SInC to generate three different sets of gene sequences with CNV region lengths ranging from 3000 to 50000 bp. For each sequence, ART ...
Because WhatsHap calculates haplotypes only for pri- mary alignment, the phased SNPs on the supplementary alignment reads sup- porting these SV were manually counted using the SAMtools (version 1.7) mpileup function. Then, we extracted the reads with ≥2 SNPs and a ratio of the number of SNPs...