Bam file format reference name how to#

In particular, we use options '-sensitive -dpad 0 -gbar 99999999 -mp 1,1 -np 1 -score-min L,0,-0.1' by default. Since currently RSEM does not handle indel, local and discordant alignments, the Bowtie2 parameters are set in a way to avoid those alignments. Use Bowtie 2 instead of Bowtie to align reads. Please refer to the SAM official website for the details of FAI format. is a FAI format file containing each reference sequence's name and length. If the header section of input alignment file does not contain reference sequence information, this option should be turned on. The exact file format will be determined automatically. Input file contains alignments in SAM/BAM/CRAM format. Both Bowtie/Bowtie2, expression estimation and 'samtools sort' will use this many threads. For Illumina TruSeq Stranded protocols, please use 'reverse'. If 'forward'/'reverse' is set, the '-norc'/'-nofw' Bowtie/Bowtie 2 option will also be enabled to avoid aligning reads to the opposite strand. 'reverse' means all (upstream) reads are derived from the reverse strand. 'forward' means all (upstream) reads are derived from the forward strand. 'none' refers to non-strand-specific protocols. It recognizes three values: 'none', 'forward', and 'reverse'. This option defines the strandedness of the RNA-Seq reads. Input reads do not contain quality scores. All output files are prefixed by this name (e.g., sample_) BASIC OPTIONS -paired-end The user must have run 'rsem-prepare-reference' with this reference_name before running this program.

Bam file format reference name how to#

See Description section for how to make input file obey RSEM's requirements. In addition, RSEM does not allow the SEQ and QUAL fields to be empty. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. RSEM requires all alignments of the same read group together. If '-' is specified for the filename, the input is instead assumed to come from standard input. If the -no-qualities option is specified, then FASTA format is expected. By default, these files are assumed to be in FASTQ format. downstream_read_file(s)Д¬omma-separated list of files containing downstream reads which are paired with the upstream reads. Rsem-calculate-expression -alignments input reference_name sample_name ARGUMENTS upstream_read_files(s)Д¬omma-separated list of files containing single-end reads or upstream reads for paired-end data. Rsem-calculate-expression -paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name SYNOPSIS rsem-calculate-expression upstream_read_file(s) reference_name sample_name Rsem-calculate-expression - Estimate gene and isoform expression from RNA-Seq data.