title

Converts a SAM or BAM file to FASTQ. This tool extracts read sequences and base quality scores from the input SAM/BAM file and outputs them in FASTQ format. This can be used by way of a pipe to run BWA MEM on unmapped BAM (uBAM) files efficiently.

samtofastq

SamToFastq

Spliced Transcripts Alignment to a Reference © Alexander Dobin, 2009-2024

star

STAR

This utility adds the following information that is lost when realigning BAM files:Copies the "read fails platform/vendor quality checks" flag (0x200) from the original BAM;Adds a read group ID to each read based on the read ID, in the format RG:Z:xxxxx.x

bamsync

RNA-SeQC 2, an efficient reimplementation of RNA-SeQC (DeLuca et al., 2012) that adds multiple metrics designed to characterize sample quality across a wide range of RNA-seq protocols.

rna-seqc

RNA-SeQC

A quality control tool for high throughput sequence data.

fastqc

FastQC

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

rsem

RSEM

Identifies duplicate reads. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.

Used By