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Looking for database to download transcriptome annotation file

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.

next-gen sequence r rna-seq
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updated by Ram Ram • written by jack jack

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."

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updated by Ram Ram • written by Ashutosh Pandey Ashutosh Pandey

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

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updated by Ram Ram • written by jack jack

1 answer

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

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written by Israel Barrantes Israel Barrantes

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