TIGAR: Transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
README.md
Tigar.jar

README.md


New version, TIGAR2, is now available. Please download and use the latest implementation.

https://github.com/nariai/tigar2


===== TIGAR

TIGAR: Transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference

Naoki Nariai, Osamu Hirose, Kaname Kojima and Masao Nagasaki

Bioinformatics. 29(18):2292-2299 (2013)

 Example: java -jar Tigar.jar FASTA SAM OUT --alpha_zero DOUBLE --is_paired INT --polyA INT
 FASTA          : reference FASTA file
 SAM            : target SAM/BAM file
 OUT            : output file
 --alpha_zero DOUBLE : tuning parameter alpha_zero
 --is_paired INT  : paired-end data. default = 0 (false). Please set 1, if sam
                  file was generated from paired-end reads.
 --polyA INT      : polyA flag. default = 0 (false). Please set 1 if both read
                  and reference sequences contain polyA tails.

New version, TIGAR2, is now available. Please download and use the latest implementation.

https://github.com/nariai/tigar2


Recommended pipeline to run TIGAR

Prepare cDNA reference sequences in FASTA format.

e.g.) human
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/refMrna.fa.gz

e.g.) mouse
http://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/refMrna.fa.gz

Build bowtie2 index

mkdir ref
bowtie2-build refMrna.fa ./ref/refMrna

Run bowtie2

bowtie2 -p 8 -k 100 --very-sensitive ./ref/refMrna sample.fastq > sample.sam

Run TIGAR

java -jar Tigar.jar refMrna.fa sample.sam --alpha_zero 0.1 sample_out.txt

Output format

ID: transcript (mRNA) ID that the program predicted

LENGTH: transcript length

Z: the number of expected fragments that the program assigned to the transcript

FPKM: normalized expression level (Fragments Per Kilobase of exon per Million mapped fragments)

THETA: estimated parameter (transcript abundance), essentially Z divided by total mapped reads.

Please note that sam files are expected to be sorted by read name. In order to sort sam files by read name:

samtools view -bS sample.sam > sample.bam
samtools sort -n sample.bam sample.prefix
samtools view -h sample.prefix.bam > sample_sorted.sam

Please note that this implementation of TIGAR requires large memory size for large sam/bam files. If you have any problems, please let me know by e-mail.

This site is maintained by: Naoki Nariai

Contact:
nariai [at] megabank.tohoku.ac.jp

Last updated on 2015/01/14