How To Visualize Spliced Alignments Of Next Gen Sequencing Data?

Question

[Darked89]

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:

• SpliceMap

See also thread on SeqAnswers

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

Answer 1

[Malcolm.Cook]

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

[Darked89]

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.

Answer 2

[Fred Fleche]

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.[?]