I'm trying to download the genome and transcriptom annotation in GTF file format for the Drosophila melanogaster. I tried the Ensemble website, but I got lost. Would someone help me to get those annotation files? Jan 23, 2017 The data released here is associated with the data release announcement on the PacBio blog. In collaboration with Dr. Casey Bergman at the University of Manchester and Drs. Susan Celniker and Roger Hoskins of the Berkeley Drosophila Genome Project (BDGP) at Lawrence Berkeley National Laboratory, we.
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- Another study reported the development of a method for scarless allele replacement in Drosophila, which was shown to be suitable for single or multiple allelic substitutions in regions of interest.
- Downloads and Resources. The header for each file contains the name of the resulting matrix ID and the flybase gene ID for the transcription factor (or factors for heterodimers). Tools for the analysis of TF binding sites within the Drosophila genome.
Jan 01, 2005 FlyBase includes information about the structure and function of genes and gene products of the Drosophila genome ( 1). FlyBase data files are available for download by ftp from several of our mirror sites, in a text, acode or XML format. I have transcriptome sequencing data in.sra format. I want to do alignment and quantification. For that, I need to have transcript file in format of Fastq which is the transcript name with it's sequence. Would someone recommend database to download the transcript file? I want for drosophila melanogaster.
Question: Looking for database to download transcriptome annotation file
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5.3 years ago by
Germany
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Hi,
I have transcriptome sequencing data in .sra format. I want to do alignment and quantification. for that, I need to have transcript file in format of Fastq which is the transcript name with it's sequence.
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Would someone recommend database to download the transcript file ? I want for drosophila melanogaster.
ADD COMMENT • link • modified 5.3 years ago by Obi Griffith ♦ 18k • written 5.3 years ago by jack • 790
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First you need to convert sra (sra) into fastq (.fastq/.fq) files. Then align fastq files against reference genome to get bam (.sam/.bam) file. Then you use that bam file and transcript annotation file (gff/gff3/gtf) to get the RPKM counts.
I couldnt understand what you mean by 'I need to have transcript file in format of Fastaq which is the transcript name with it's sequence. '
ADD REPLY • link written 5.3 years ago by Ashutosh Pandey ♦ 11k
I'm using the sailfish for quantification. it does not need reference genome, it only does need reference transcriptome.
ADD REPLY • link written 5.3 years ago by jack • 790
What is GenomeRNAi?
GenomeRNAi is a database containing phenotypes from RNAinterference (RNAi) screens in Drosophila andHomo sapiens. In addition, the database provides an updated resourceof RNAi reagents and theirpredicted quality.
RNAi screening data is extracted from the literature by manual curation.
Please remember tocite GenomeRNAito help us secure future funding. We also appreciate yourfeedback and suggestions!
xE2x80在y RNAi identifier
..by screen
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the GenomeRNAi database eitherby viewing all screens,by looking at frequent hitters or by choosing an example below
Reagents: DRSC03504,BKN25930
News
- GenomeRNAi v17 released27 November, 2017
GenomeRNAi version 17.0 contains a total of 687 RNAi screen: 478 in human and in 209 Drosophila. In order to facilitate the submission and release process, from now it is possible to visualize submitted screens and publications also before the new database version is released. For performance and availability, We switched from DAS to the currently popular bioinformatics file formats bigbed and 2bit in the Genome browser.
Many thanks to Falkenberg et al. that submitted a screen on an anti-cancer agent sensitivity and to all the users of GenomeRNAi that sent us feedbacks and reactions.
Please cite: Schmidt et al. (2012). GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update.