Question: Which aligment tool is best for eukaryotic transcriptome?
1
gravatar for sudha
8 months ago by
sudha20
sudha20 wrote:

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!

sequencing rna-seq alignment • 343 views
ADD COMMENTlink modified 8 months ago by genomax55k • written 8 months ago by sudha20
3

STAR is a good starter.

ADD REPLYlink written 8 months ago by arta540
2
gravatar for Macspider
8 months ago by
Macspider2.5k
Vienna - BOKU
Macspider2.5k wrote:

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)
ADD COMMENTlink modified 8 months ago • written 8 months ago by Macspider2.5k
2

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) !

ADD REPLYlink written 8 months ago by lieven.sterck2.3k
1

You are right, that is what I meant, my bad.

ADD REPLYlink written 8 months ago by Macspider2.5k
1

Thanks a lot for your answers, it made my day!

but (for alignment) RSEM uses bowtie2 only right ?

ADD REPLYlink modified 8 months ago • written 8 months ago by sudha20
1

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.

ADD REPLYlink written 8 months ago by Macspider2.5k
2
gravatar for Carlo Yague
8 months ago by
Carlo Yague4.2k
Belgium
Carlo Yague4.2k wrote:

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.

ADD COMMENTlink written 8 months ago by Carlo Yague4.2k
2
gravatar for genomax
8 months ago by
genomax55k
United States
genomax55k wrote:

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.

ADD COMMENTlink modified 8 months ago • written 8 months ago by genomax55k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1307 users visited in the last hour