MacManes Blog http://macmanes.com/blog Evolutionary Biology, Next-Gen Sequencing, Population Genetics Thu, 06 Oct 2011 15:20:54 +0000 en hourly 1 http://wordpress.org/?v=3.2.1 Assemblathon 2 ‘bird’ Stats http://macmanes.com/blog/?p=27 http://macmanes.com/blog/?p=27#comments Thu, 06 Oct 2011 15:20:54 +0000 macmanes http://macmanes.com/blog/?p=27 Here are the basic assembly stats for the bird data:  contig cutoff size=250bp

 

N:250 n:N50 N80 N50 N20 max sum name Average 105054.3 8628.2 1235754.8 3899483.5 9540090.4 19342630.9 1.03E+09 849 57 2283 8580 20266 51162 1933317 bird_8C_contigs.fa 826 47 2930 11620 23347 57581 2026432 bird_8C_scaffolds.fa 70467 7137 15629 39414 87076 554547 1.04E+009 bird_6C_contigs.fa 16495 [...]]]> Here are the basic assembly stats for the bird data:  contig cutoff size=250bp

 


 N:250 n:N50 N80 N50 N20 max sum name
Average 105054.3 8628.2 1235754.8 3899483.5 9540090.4 19342630.9 1.03E+09

849 57 2283 8580 20266 51162 1933317 bird_8C_contigs.fa

826 47 2930 11620 23347 57581 2026432 bird_8C_scaffolds.fa

70467 7137 15629 39414 87076 554547 1.04E+009 bird_6C_contigs.fa

16495 32 3207491 10011138 19098421 49826764 1.04E+009 bird_6C_scaffolds.fa

37670 4312 25386 67833 146481 671540 1.06E+009 bird_7C_contigs.fa

8062 23 2481996 10935449 37556899 50983430 1.06E+009 bird_7C_scaffolds.fa

190778 16265 6158 18177 38632 235482 1.07E+009 bird_10C_contigs.fa

92853 81 228034 2965671 8717439 32814605 1.07E+009 bird_10C_scaffolds.fa

54037 4855 18956 56996 141343 712654 1.10E+009 bird_11C_contigs.fa

4341 18 1833827 16806221 42927674 64643934 1.10E+009 bird_11C_scaffolds.fa

65217 5939 21833 53463 107654 666240 1.11E+009 bird_13E_contigs.fa

10697 23 6275406 14199076 31408994 65236555 1.11E+009 bird_13E_scaffolds.fa

66411 6094 20919 52129 105709 500974 1.11E+009 bird_14E_contigs.fa

10685 23 6278647 14202455 31417212 65264275 1.11E+009 bird_14E_scaffolds.fa

92575 7505 13282 39267 88316 666240 1.11E+009 bird_12C_contigs.fa

10703 23 6286291 14221761 31447220 65359764 1.11E+009 bird_12C_scaffolds.fa

75487 8235 16695 41221 80970 465622 1.17E+009 bird_4C_contigs.fa

34104 638 157708 516390 1104665 2942284 1.17E+009 bird_4C_scaffolds.fa

88197 2156 32923 134986 342996 1818605 1.17E+009 bird_3E_contigs.fa

41941 22 4805477 14768158 35825618 67706724 1.17E+009 bird_3E_scaffolds.fa

84487 1383 40265 193162 559349 2740960 1.17E+009 bird_2C_contigs.fa

41941 22 4815185 14777158 35841802 67755865 1.17E+009 bird_2C_scaffolds.fa

77515 3165 31975 102941 220703 849043 1.19E+009 bird_9C_contigs.fa

54666 177 405855 1746932 4194166 11487706 1.19E+009 bird_9C_scaffolds.fa

346930 5356 4039 50966 170544 1468602 1.31E+009 bird_1C_contigs.fa

293817 270 17136 894118 4140394 19295806 1.31E+009 bird_1C_scaffolds.fa

175676 21521 10126 23871 50265 424718 1.84E+009 bird_5C_contigs.fa

130759 7527 13236 38683 323074 4670483 1.84E+009 bird_5C_scaffolds.fa

486721 77970 1478 3334 7742 203381 9.98E+006 bird_15C_contigs.fa

486721 77970 1478 3334 7742 203381 9.98E+006 bird_15C_scaffolds.fa
]]> http://macmanes.com/blog/?feed=rss2&p=27 1 Promiscuity in mice is associated with increased vaginal bacterial diversity http://macmanes.com/blog/?p=22 http://macmanes.com/blog/?p=22#comments Tue, 04 Oct 2011 00:54:11 +0000 macmanes http://macmanes.com/blog/?p=22 I thought I’d add a link to my newest paper: (http://dx.doi.org/10.1007/s00114-011-0848-2)

Abstract:

Differences in the number of sexual partners (i.e., mating system) have the potential to exert a strong influence on the bacterial communities present in reproductive structures like the vagina. Because this structure serves as a conduit for gametes, bacteria present there may have [...]]]> I thought I’d add a link to my newest paper: (http://dx.doi.org/10.1007/s00114-011-0848-2)

Abstract:

Differences in the number of sexual partners (i.e., mating system) have the potential to exert a strong influence on the bacterial communities present in reproductive structures like the vagina. Because this structure serves as a conduit for gametes, bacteria present there may have a pronounced, direct effect on host reproductive success. As a first step towards the identification of the relationship between sexual behavior and potentially pathogenic bacterial communities inhabiting vital reproductive structures, as well as their potential effects on fitness, I sought to quantify differences in bacterial diversity in a promiscuous and monogamous mammal species. To accomplish this, I used two sympatric species ofPeromyscus rodents—Peromyscus californicus and Peromyscus maniculatus that differ with regard to the number of sexual partners per individual to test the hypothesis that bacterial diversity should be greater in the promiscuous P. maniculatus relative to the monogamous P. californicus. As predicted, phylogenetically controlled and operational taxonomic unit-based indices of bacterial diversity indicated that diversity is greater in the promiscuous species. These results provide important new insights into the effects of mating system on bacterial diversity in free-living vertebrates, and may suggest a potential cost of promiscuity.

]]> http://macmanes.com/blog/?feed=rss2&p=22 0 update http://macmanes.com/blog/?p=8 http://macmanes.com/blog/?p=8#comments Sun, 02 May 2010 09:16:58 +0000 macmanes http://macmanes.com/blog/?p=8 Well, it’s certainly been a long time since ive written anything here, and I won’t claim to be up you giving a full update now… besides, it seems that a grand total of 2 people look at this non-existant blog, and that includes me..

I guess this is that I get for trying to finish [...]]]> Well, it’s certainly been a long time since ive written anything here, and I won’t claim to be up you giving a full update now… besides, it seems that a grand total of 2 people look at this non-existant blog, and that includes me..

I guess this is that I get for trying to finish my PhD..

Anyways, I’m knee deep in Illumina data, having 2 lanes of mRNA-seq and another 2 of genomic dna.. For reasons of memory availability- i’v e been using ABySS, but have been trying to use SOAPdenovo, and RAY, and dreaming of VELVET..

The dissertation is coming along nicely… I’ve been working a lot with the program HYPHY for a lot of the positive selection stuff.. A few chapters competed this summer and submitted to journals… Lookls like im on track for a December 2010 finish.. 7 months from now!!

Oh yeah, Evolution meeting and a small by invitation only symposium in france in October…

]]> http://macmanes.com/blog/?feed=rss2&p=8 0 toll like receptors… http://macmanes.com/blog/?p=7 http://macmanes.com/blog/?p=7#comments Tue, 13 Oct 2009 22:03:31 +0000 macmanes http://macmanes.com/blog/?p=7 I was thinking about doing a small project looking at selection on genes associated with innate immunity- like the TLR family.. Might serve as a nice contrast to all my work with the MHC..

What do you all think about that??

]]> I was thinking about doing a small project looking at selection on genes associated with innate immunity- like the TLR family.. Might serve as a nice contrast to all my work with the MHC..

What do you all think about that??

]]> http://macmanes.com/blog/?feed=rss2&p=7 0 Intro http://macmanes.com/blog/?p=5 http://macmanes.com/blog/?p=5#comments Sat, 10 Oct 2009 07:17:37 +0000 macmanes http://macmanes.com/blog/?p=5 Not sure how much Im going to write here, but…

]]> Not sure how much Im going to write here, but…

]]> http://macmanes.com/blog/?feed=rss2&p=5 0