Hi Lieven, With my new student Alexander Schober, we've become very interested in new tracks that have appeared in Genome View. However, we're not quite sure what we are looking at. Let's take Esi0207_0011 as a (purely random) example. 1) Can you explain to us what the pinkish track (e.g. sctg11.sort.bam) exactly is? Are we correct in thinking these are RNAseq data (single reads, non paired-end?) 2) Same question for "junctions": are these intron-exon borders mapped based on the above RNAseq reads? 3) on the sctg11.sort.bam track, is it significant that some reads (the blue ones) are mapped in reverse orientation, when the gene is obviously on the + strand? 4) if we want to look in detail at one RNAseq read or at a junction (e.g. to check some alternative splicing, funky LRR recombination, or the mismatch at 1125201), can we easily retrieve the correponding sequence from somewhere? Sorry to ask so many questions, but at least this time, I haven't accidentally hacked into BOGAS! Best, Claire ++++++++++++++++++++++++++++++++++++ Dr Claire GACHON Principal Investigator in Molecular Phycology Scottish Association for Marine Science Scottish Marine Institute PA37 1QA Oban United Kingdom claire.gachon@sams.ac.uk Skype contact : claire.gachon Tel: 0044 16 31 559 318 Fax 0044 16 31 559 001 http://www.sams.ac.uk/claire-gachon <http://www.sams.ac.uk/claire-gachon%0b>+++++++++++++++++++++++++++++++ The Scottish Association for Marine Science (SAMS) is registered in Scotland as a Company Limited by Guarantee (SC009292) and is a registered charity (9206). SAMS has an actively trading wholly owned subsidiary company: SAMS Research Services Ltd a Limited Company (SC224404). All Companies in the group are registered in Scotland and share a registered office at Scottish Marine Institute, Oban Argyll PA37 1QA. The content of this message may contain personal views which are not the views of SAMS unless specifically stated. Please note that all email traffic is monitored for purposes of security and spam filtering. As such individual emails may be examined in more detail.