Question: How To Visualize Spliced Alignments Of Next Gen Sequencing Data?
gravatar for Darked89
8.9 years ago by
Barcelona, Spain
Darked894.2k wrote:

I got a bunch of Illumina lanes from RNA-Seq experiment and corresponding draft genome sequence. There are few alignment programs I can use which can handle splicing:

  • Tophat (works, requires filtering short reads from fastq)
  • GEM (works, tabulated output, some manual output combining required)
  • SOAPals (works on example data, genome indexing fails on my input)

So far I am aware of only one program able to display spliced alignments (SeqMonk) but have not managed to run it yet.

My question: are there any other programs for next gen spliced mapping visualization? If yes, which input formats they use?

EDIT: One more new tool for spliced mapping:

See also thread on SeqAnswers

SpliceMap works on test data, strange format of input reads.

ADD COMMENTlink modified 6 months ago by RamRS20k • written 8.9 years ago by Darked894.2k
gravatar for Malcolm.Cook
8.9 years ago by
kansas, usa
Malcolm.Cook1.0k wrote:

IGV displays the spliced alignments present in TopHat's BAM file just fine.

ADD COMMENTlink written 8.9 years ago by Malcolm.Cook1.0k

Thank you! I works. :). One note: I got from Tophat junctions.bed, coverage.wig, accepted_hits.sam. The last one I converted using samtools, but for that I needed to create tab file with seq_names seq_lengths. Finally IGV loads only indexed files. I will describe whole procedure tomorrow.

ADD REPLYlink written 8.9 years ago by Darked894.2k
gravatar for Fred Fleche
8.9 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

I don't know if it is interesting in your case (next gen) but I used to work with Spidey available trough a web interface or an executable at the NCBI. [?]The Genomic sequence has to be a fasta sequence or GI/Accession and the same for the mRNA sequence(s) that you want to align.[?]

ADD COMMENTlink written 8.9 years ago by Fred Fleche4.3k
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