Looking for database to download transcriptome annotation file

Question

[jack]

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.

Would someone recommend database to download the transcript file? I want for drosophila melanogaster.

[Ashutosh Pandey]

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 couldn't understand what you mean by "I need to have transcript file in format of Fastaq which is the transcript name with it's sequence."

[jack]

I'm using the sailfish for quantification. It does not need reference genome, it only does need reference transcriptome.

Answer 1

[Israel Barrantes]

Here you can find links to species' specific annotations (including Drosophila), and with the GFF/GTFs there you can easily extract the transcriptome from the genomic fasta

[KVC_bioinfo]

can not open the link