A function to extract pair end reads from the bam file generated with subread functionRaffaele A Calogero
A sorted bam fileprocess_bam(bamfile, threads) A standard fastq fileprocess_fastq_plain(fastqfile, 'threads') A fastq file with metadata from MinKNOW or Albacoreprocess_fastq_rich(fastqfile) A sequencing_summary file generated by Albacoreprocess_summary(sequencing_summary.txt, 'readtype') ...
Format: FASTQ (default) or FASTA Basecall-anchored modified base scores are also available in hts-spec BAM format tags (--outputs mod_basecalls). Mappings Format: SAM, BAM (default), or CRAM A tab-separated mapping text summary is also produced including per-read alignment statistics. ...
The raw sequencing data (FASTQ files) were subjected to a quality control using the FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and subsequently were aligned against the human genome (hg19 assembly) using Hisat2 (http://daehwankimlab.github.io/hisat2/) with ...
Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34: i884– 90. Google Scholar Crossref PubMed WorldCat 54. Grabherr MG, Haas BJ, Yassour M et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; ...
Extract subsets of ONT (Nanopore) reads based on time Usage: ontime [OPTIONS] <FILE> Arguments: <FILE> Input fastq/fasta/BAM/SAM file Options: -o, --output <FILE> Output file name [default: stdout] -O, --output-type (fastq/a output only) u: uncompressed; b: Bzip2; g: Gzip...
bwa mem -5SP contigs.fasta.gz hic_paired.fastq.gz|\ samtools view -bS ->hic2ctg_unsorted.bam 3. Sort the resulting "Hi-C to contigs" BAM file in name order Downstream, bin3C expects read-pairs to come sequentially which requires the BAM file be sorted in name order. In future, we...
FastQC (Version 0.12.0) was used for quality control of the high-throughput sequencing data (FASTQ files) from the CTRL, PRRSV, and PRRSV+CS samples. Trimmomatic (version 0.32) was employed to trim, crop, and remove adapters from the Illumina FASTQ data, facilitating downstream analysis. The...
In addition to BWA, this self-consistent package also comes with bwa-associated and 3rd-party tools for proper BAM-to-FASTQ conversion, mapping to ALT contigs, adapter triming, duplicate marking, HLA typing and associated data files. Seeking help The detailed usage is described in the man page...
samblasteris a fast and flexible program for marking duplicates inread-id grouped1paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates,samblaster...