Jan

28

Transcriptome Sequencing of Non-model Species

Filed Under Information 

Eastern Diamondback Rattlesnake (Conus bullatus)
Protozoan Parasite (Plasmodium falciparum)
Périgord Black Truffle (Tuber melanosporum)
Migratory Locust (Locusta migratoria)
Mosquito (Anopheles funestus)
Milkweed Bug (Oncopeltus fasciatus)
Greenhouse Whitefly (Trialeurodes vaporariorum)
Pigeon Pea (Cajanus Cajan)
Buckwheat (Fagopyrum)
Mungbean (Vigna radiata)
Copepod (Tigriopus californicus)
Freshwater Planarian (Schmidtea mediterranea)
Black Cohosh (Actaea racemosa)
Sweet Potato (Ipomoea batatas)

Incoming search terms:

  • cuffdiff ribozero plasmodium
  • copepod transcriptome
  • DGE non model species RNA-seq
  • non-model plant transcriptome assembly
  • rna sequencing for non model plants
  • rna sequencing non model species
  • sweet potato RNA seq
  • transcriptome rna seq insect
  • transcriptome sequencing species

Comments

2 Responses to “Transcriptome Sequencing of Non-model Species”

  1. GANESH on May 4th, 2012 2:14 am

    Sir,please send me some research paper for total RNA Transcriptome Sequencing of mung bean.

  2. transcriptome on June 14th, 2012 12:07 pm

    thanks

Leave a Reply




  • Social Networking Pages

    Linkedin Group

  • Follow Me on Pinterest

  • RSS SEQanswers – RNA Sequencing

    • CuffDiff strange output May 23, 2013
      Hi, I hope that someone can be so gentle to help me. I'm analizing some data from RNA-Seq with TopHat and Cufflinks and I focus my attention on... […]
      Pruexel
    • cannot away with cuffdiff,incredible May 23, 2013
      Hi,all I have 4(A,B,C,D) sample in 4 times(increasing time),I got diff result in 3 different cuffdiff 1.cuffdiff 3(A,B,C) individual... […]
      upper
    • TopHat extremely low paired mapping rate. PLS HELP! May 22, 2013
      Hey guys, I have some problems with my paried-end RNA seq analysis on Galaxy. As you can see in the bam flagstat output, my tophat alignment rate is... […]
      Felix.Lee
    • Identifying small RNA sequence within whole genome sequence May 21, 2013
      Hi all, I want to know if there are any useful bioinformatic tool to find small RNA sequence within a whole bacteria genome. Thank you in... […]
      Inma
    • standard of clean data May 21, 2013
      Hi all I recently got my prokaryotes RNA-seq data report back. the standard filter steps of the raw data set by our local sequencing center is as... […]
      Pengfei Liu
    • Problem with cummeRbund diffData() May 20, 2013
      Hi all, I'm running Tophat/cufflinks/cuffdiff for differential gene expression and analysis with cummeRbund (v 2.0.0). I'm having an issue with... […]
      Enrique Zudaire

  • RSS Biostar – RNA-Seq

    • Why am I getting so many unmapped reads in STAR, classified as "too short"?
      I am currently using STAR to map several Hi-SEQ mRNA runs. I'm having trouble getting a decent amount of reads to map, but I don't really understand why. I'm hoping you can shed some light :) In the final log, only about 50% (or less) of the reads map to the reference. I'm using a GTF in addition to the genome. The unmapped bin that most […]
    • What are the best practices for SNP identification in RNA seq transcriptome data
      I have 20 RICE RNA seq tranascriptome data hiseq 2000 platform paired end reads. I aligned fasta reads with BWA and remove PCR duplicates with PICARD. Later I call SNP with samtools using various parameters. I would like to clarify what parameters should I used while alinging to reference rice genome for looking SNP location 100 bp upstream and 250 bp downst […]
    • How do TopHat options -g , --supress-hits, and Bowtie options interplay?
      Hi, I am currently using TopHat2 to map RNA-seq runs. I think there have been some changes pertaining the -g option. Does anyone know how it works now? I used to think that setting -g would look for n alignments for a given read, report them [if top-scoring] and discard those reads that had more than g [top scoring] alignments. Now, the description sounds mo […]
    • What happened to -k in TopHat for multiple-mapping reads?
      Selecting -g n in tophat does not discard reads mapping more than n, but instead only reports n alignments for those out all all their TOP scoring alignments. I think there used to be an option -k that would allow one to discard reads that topped x alignments -- whatever happened to that? I only see -g in the tophat 2 manual, no reporting options like before […]
    • Does tophat use the library-type information for mapping, or just for the XS flag?
      When I specify library-type to TopHat, i.e., first-strand, second-strand, unstranded, TopHat appends a value + or - to the XS:A flag, which is useful for subsequent analyses, such as annotation. However, does this information actually influence the "mappability" of reads, or is this unaffected? My thinking is that the information would be considere […]
    • Purpose of Y-shaped adapters in Illumina Sequencing?
      Hi all, Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library. The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary. What are the advantages of this? My take of this over having fully-complementary adapters (ADAPTER1 - - - - - ADAPTER1) is that: -Upon primer a […]