Dear one, Which alignment tool is best to align eukaryotic (homo sapiens) transcriptome? Please comment your answer with reason why! Thanks in advance!
p.s. My sequences are paired end & human samples! My intention is to do differential gene expression study!
p.s. I have seen that there are many alignment tools are used and given in publications, so confused a lot! I am new to bioinformatics!
3 answers
Alignment of RNASeq reads on a genomic reference
- STAR (link) -> super-fast, gold standard for many people, awesome 2-pass mode (see manual)
- HISAT2 (link) -> same as Tophat2, much, much faster, good precision
- BWA (link) -> handles well also supplementary alignments (2048 bitwise flag) to then retrieve chimeras
all handle spliced alignment
Alignment of RNASeq reads on a transcriptomic reference
- RSEM (link) -> accurate quantification of gene and isoform expression (probably your best choice, imho, for this)
Yeah, or bowtie 1, if you specify it. But it works quite fine, imho. However, you can use HISAT2 on transcriptome references tailoring the output directly for cufflinks (--dta-cufflinks) if this helps you.
personally don't agree with the "all handle spliced alignment" statement , they all can handle split or gapped alignment but that's a totally different thing than spliced alignment (== splice-site aware aligner) !
You are right, that is what I meant, my bad.
You should also consider pseudo-alignments tools, such as kallisto and salmon. They are extremely fast and lightweight, can quantify millions of reads under a few minutes on a laptop computer.
BBMap suite (includes scanning/trimming program bbduk.sh and many things other than the aligner, which is bbmap.sh). I will not enumerate its advantages, since they should be apparent, if/when you try it.
Many aligners will need ~ 30G of RAM for human genome. If you don't have that available then bwa may be the one to try. It minimally needs ~6 G RAM.
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STAR is a good starter.