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
+++++++++++++++++++++++++++++++

 

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