---

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

https://github.com/nariai/tigar2

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===== 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