Two Big Contigs, and No Hints

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nragland
Posts: 10
Joined: Sun Feb 04, 2007 10:39 pm
Location: St. Edward's University, Austin TX

Two Big Contigs, and No Hints

Post by nragland » Tue Feb 13, 2007 12:33 am

Below is an image of one of my student's initial assembly view. She has two large contigs with no fw/rev pairs spanning any gaps and no crossmatch results. She has picked primers to run off the ends of both contigs.

I could not find the GTGATTC end clone indicator on her end reads.

Any ideas or suggestions would be appreciated. Thanks


Image

cjones
Posts: 99
Joined: Sun Feb 04, 2007 10:19 pm
Location: Moravian College, Bethlehem PA
Contact:

Post by cjones » Tue Feb 13, 2007 3:25 am

The first thing I'd try is to find the XBAB read (or reads -- there should be two, but many fosmids seem to have only one, which the folks at WashU are aware of and working on). Those reads are at the ends of the fosmid, so if you're lucky and have two, that will give you your relative orientations.
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

cshaffer
Posts: 211
Joined: Sun Feb 04, 2007 10:29 pm
Location: Washington University in St Louis
Contact:

end reads

Post by cshaffer » Tue Feb 13, 2007 8:51 pm

There are also the original fosmid reads from the agencourt data that should be at the ends. If you cannot find the reads that start XBAB you can try to find the original end reads. We only picked fosmids where both end sequences worked so they should both be in the assembly somewhere (of course since different assemblers were used it is always a possibility that these ends will not get assembled but it should be pretty rare).

Here is the table of GEP name vs. Agencourt name; not all these projects are available but you should be able to find your project here and then find the agencourt name. The reads off the end of this will have the leading 0000 removed and a .b1 and .g1 added to the end. Thus the end reads for project 105-O01 will be 38892000O01.b1 and 38892000O01.g1

Code: Select all

105-O01	000038892000O01
110-B13	000038978500B13
118-J09	000039103900J09
120-D14	000039061900D14
123-N24	000039102200N24
130-G02	000039059900G02
133-D08	000039104200D08
140-O13	000039025200O13
145-P18	000038866400P18
150-G05	000038917900G05
155-C22	000039060200C22
160-I01	000038978300I01
165-G05	000038979500G05
170-M23	000039089900M23
175-P12	000038867700P12
180-B08	000038867500B08
187-O13	000038889200O13
190-K08	000039090300K08
195-G04	000038978600G04
200-N19	000039024300N19
205-H09	000039024100H09
210-H10	000038919600H10
215-F05	000038988600F05
216-A22	000039102400A22
218-P06	000039052000P06
225-M13	000039050400M13
230-A21	000039059600A21
235-I16	000039089800I16
240-J07	000038892100J07
245-F12	000039102800F12
250-J02	000039025200J02
255-B13	000039104200B13
260-P17	000039134900P17
265-F07	000039025300F07
270-N07	000039025300N07
275-A01	000038889400A01
280-G02	000039025600G02
290-D14	000038863500D14
295-A10	000038918600A10
300-M15	000039154700M15
305-N24	000039135100N24
310-B11	000039154400B11
312-B23	000038989000B23
314-H01	000039102400H01
318-A21	000039025200A21
325-M22	000039154500M22
330-A17	000038988000A17
335-G18	000039102200G18
335-I06	000039102300I06
340-H14	000039090100H14
345-C05	000039134400C05
348-O18	000038982500O18
355-J17	000039050100J17
360-I02	000038889800I02
365-C24	000038988400C24
368-B17	000039103500B17
375-B20	000038960300B20
380-A10	000039134900A10
387-L12	000038982100L12
390-J23	000038867500J23
395-O06	000039061100O06
400-O10	000038978100O10
405-G11	000039023500G11
410-C08	000038961200C08
415-E23	000039155700E23
420-O08	000038918900O08
425-E07	000039155200E07
430-O17	000039061600O17
433-D06	000039025000D06
440-B24	000039090200B24
445-G19	000039136100G19
450-M05	000039052300M05
455-J01	000039025200J01
460-B17	000039050800B17
465-C16	000039061900C16
470-O16	000038867200O16
475-L12	000038978800L12
480-D14	000038866700D14
485-B16	000039025200B16
488-C15	000038960300C15
495-D24	000038988400D24
500-E20	000039025700E20
503-I18	000039134500I18
510-L04	000039135500L04

abenjamin
Posts: 5
Joined: Sun Feb 04, 2007 10:36 pm

a pair of my students also had the same project

Post by abenjamin » Wed Apr 04, 2007 6:12 pm

Hello! Two of my students had the same project and we are having difficulty joining the contigs. Did your student ever end up joining the two? Thanks!

Ashlee

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