22 Questions 66 Answers 0 Followers
Questions related from Fang Liu
Dear all, One of my friends has to amplify some species-specific genes from cooking oil, which contained little and mostly degraded DNA. I think paleontologists often work on degraded ancient DNA....
07 July 2016 2,968 5 View
Dear all, I am interested in finding the core genome and singleton genes from a dataset of multiple chloroplast genomes (n=12). I don't have much experience in bidirectional BLAST. Can anyone...
07 July 2016 2,231 2 View
Can anyone send me the PDF? Thanks
05 May 2016 2,438 2 View
Hello, I know tef can be used as a phylogenetic marker for fungi. But what about other organisms? For eukaryotes, 18S rRNA is definitely too conservative in many cases. By the way, COI is used in...
02 February 2016 3,874 2 View
Hello, my data is from a functional DNA array and it looks like this : phylum SCC1 SCC2 SCC3 SDC1 SDC2 SDC3 SAC1 SAC2 SAC3 Verrucomicrobia 0.525962728 0.453958735 ...
12 December 2015 5,475 4 View
http://enveomics.blogspot.com/2012/11/semantics.html As showed above, this is a collection of handy scripts but haven't been deposited in github. I tried to find the dropbox download link but I...
08 August 2015 8,754 3 View
Hi everyone, I just started to use kmernorm to improve the single-cell assembly process. But after I finished, I didn't find any output (no new files or modified reads files). From the help menu,...
05 May 2015 9,218 0 View
Dear all, I don't have much experience of RNA-seq. I noticed that the reads number of one treatment (3 individuals) was lower than the other treatment. Similarly, the signal intensity of samples...
05 May 2015 3,295 9 View
Hi guys, I used laser-capture-microdissection (LCM) to pick the sponge-associated filamentous bacterial cells. Then I followed the instruction of QIAGEN repli-g single cell Kit to amplify the...
02 February 2015 2,491 11 View
Hi guys, I am doing a metatranscriptome study on marine sponges. In previous researches, the fungal rRNA genes and other fungal biogeochemical gene transcripts were detected by PCR and Geochip....
02 February 2015 6,109 5 View
Hi guys, just a random question. As HGT frequently happen in microbial world, could house-keeping genes, e.g. gyrB, COI, rRNA be horizontally transferred between microbes? Any input is...
01 January 2015 3,618 7 View
Hi guys, I am using MacOS 10.9.4 with Xcode 5.1 (command line tools installed) Today I upgraded macports and installed py27-numpy. Everything looked ok in my terminal window. Then I tried to...
07 July 2014 895 10 View
Hi guys, I don't now the meaning of BT in the table. I've done some HiSeq projects but it's the first time to see BT. Any ideas? Thanks
07 July 2014 1,695 0 View
Hey guys, I am helping a coworker to build a fungal phylogenetic tree. In brief, the sequences were amplified by EF4/FUNG5 from ocean environmental DNA. Clone libraries were constructed and the...
07 July 2014 6,895 5 View
Hi guys, I am pretty sure that some strains have similar 16S rRNA sequences but have distinct metabolic repertoires. But I couldn't find any paper discussing about that. If you have a copy of this...
06 June 2014 6,460 2 View
I am processing fungal LSU 454 data using Mothur 1.31. I used LR0R/LR3 to amplify ca.600bp of fungal LSU. It really shocks me that the command pre.cluster (Environ Microbiol. 2010 July; 12(7):...
04 April 2014 4,657 3 View
I am analysing my sponge meta-transcripts data obtained from GeoChip. According to my data, at least over 1000 fungal genes showed transcriptional activity, most of them are assigned to...
01 January 2014 8,494 3 View
Just had a little discussion with my co workers. And both of us were not sure about the definition of filamentous fungi. Can anybody show me some solid evidence/definition about filamentous fungi?
01 January 2014 5,643 9 View
I just downloaded an alignment of fungal EF1a from AFTOL (http://wasabi.lutzonilab.net/pub/alignments/download_alignments). But it's in nex format which I've never seen before. Now I want to...
12 December 2013 2,586 3 View
I am going to use D1-D2 domain for barcoding sponge-associated fungi. My primer choice is LR0R&LR3, generating 600bp products. But I didn't see any articles talking about the cutoff for 28S rRNA...
11 November 2013 10,048 2 View
I found in MEGA5, after bootstrap test, there was no scale bar in my bootstrap consensus tree. While in the original tree, there was a scale bar. Does anyone know why this happens in MEGA5?
10 October 2013 1,539 3 View
I am studying the active fungi in marine sponges. According to this paper...
09 September 2013 1,382 2 View
