BamTools

[…] polymorphisms were then used as a guide for the haplotyping procedure. The program is written in C++ as a standalone program. To access bam files and retrieve reads aligned to specific locations, the bamtools API is used (). First, all haplotypes for each accession are collected at every two-position haplotype where there is a potential polymorphism at both sites within a specified base window. Ha […]

[…] SAT2 with the parameters “--dta-cufflinks --rna-strandness RF -k 5 --no-mixed --no-discordant --sp 1000,1000.” Properly (i.e., convergent read pairs) and uniquely mapped reads were selected using the BAMtools “filter” command and SAMTools “view” command with the parameter “-q 40.” For genome-guided transcriptome assembly, Cufflinks was used with the parameters “--multi-read-correct --frag-bias-cor […]

[…] y of being damaged using mapDamage V2.0 (Jónsson, Ginolhac, Schubert, Johnson, & Orlando, ). We sorted the aligned reads of each individual according to their position on the reference catalogue with BamTools (Barnett, Garrison, Quinlan, Strömberg, & Marth, ), and we excluded PCR duplicates by eliminating fragments starting and ending at the same positions using SAMtools V0.1.19 (Li et al., ).For […]

[…] lus.GRCm38) downloaded from Ensembl. The raw fastq data were subjected to quality trimming using Sickle, for a minimum length of 50. HISAT2 [] was used to map the reads on the genome. SAMtools [] and BAMtools [] were used to convert and sort the BAM files. HTSeq [] was used to count the reads. […]

[…] of Bowtie2 and calculated the percentage of mapped reads, mapped reads with a mapping quality > = 10 and the percentage of proper paired reads with a mapping quality > = 10 using samtools v0.1.19 and bamTools v2.3.0 []. We calculated the scaffold NG50 and the error corrected NG50 using GAGE. The error corrected NG50 corresponds to the NG50 value computed on sequences broken at each misassembly. Ad […]

[…] rg/cms/index.php?page=trimmomatic). Alignment to hg19 was done with BWA MEM v0.7.8 (https://github.com/lh3/bwa). BAM files were refined using PicardTools’ MarkDuplicates and FixMateInformation tools, BamTools filter tool (https://github.com/pezmaster31/bamtools), and GATK’s RealignerTargetCreator, IndelRealigner, and BaseRecalibrator (v3.2-2; https://www.broadinstitute.org/gatk/download/). WES som […]