Register FAQ Members List Calendar Search Today's Posts Mark Forums Read

 Similar Threads Thread Thread Starter Forum Replies Last Post boetsie Bioinformatics 252 03-07-2019 04:19 AM AdrianP Bioinformatics 0 07-02-2013 01:16 PM seb.lees Bioinformatics 0 05-28-2013 09:40 AM swe Bioinformatics 1 05-28-2013 07:27 AM pmiguel Bioinformatics 25 11-21-2011 07:26 AM

 07-23-2013, 08:42 AM #1 szimmerman Junior Member   Location: United States Join Date: Jul 2013 Posts: 7 SSPACE help Hi everyone, I was just wondering what an f_tig meant in the .evidence file produced by SSPACE. Is it the original contigs that are put into a scaffold or something else? Thanks!
 07-23-2013, 09:56 AM #2 boetsie Senior Member   Location: NL, Leiden Join Date: Feb 2010 Posts: 245 These are the original contigs (order is based on the order of the contig in the fasta file). The 'f' indicates that it has forward orientation in the final scaffold, the 'r' means the reverse orientation.
 10-18-2013, 06:41 AM #4 boetsie Senior Member   Location: NL, Leiden Join Date: Feb 2010 Posts: 245 The negative gap indicates a potential overlap between the two contigs. However, it seems unlikely that there is 615bp overlap between the contigs, indicating that the insert size you've provided in the library file is not correct. To illustrate how this is estimated; Say you have a two contigs, contig1 of 1000bp and contig2 of 2000bp, one of your paired-read aligns at position 900 at contig1 and the other at position 100 on contig 2. If you set the insert size to 210bp, the estimated gap is; Provided insert size - ((size of contig1)-(position of read1 on contig1)) + (position of read2 on contig2). In this case it is; 210 - (1000-900) + 100 = 10 So a gap of 10bp. If we change the insert size to 2000, it is; 2000 - (1000-900) + 100 = 1800 If we change the insert size to 100, it is; 100 - (1000-900) + 100 = -100 As you can see, the estimated gap really depends on the provided insert size by the user. In your case I see a number of large negative gaps, this is highly unusual. Probably you should lower your insert-size by 600 bases. Regards, Boetsie
 10-18-2013, 08:39 AM #5 Yue Xu Member   Location: china Join Date: Jun 2013 Posts: 16 Hi, thank your detailed reply, because of your reply, I understand how to calculate the gap between contigs in SSPACE. Thank you very much. But I have seen your writing formula: Provided insert size - (((size of contig1)-(position of read1 on contig1)) + (position of read2 on contig2)) whether is it lack of a pair of bracket that I mark it in the type of bold and italic? yours sincercely, Yue Xu