Looking for database to download transcriptome annotation file
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8.5 years ago
jack ▴ 960

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 • 3.5k views
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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 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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I'm using the sailfish for quantification. It does not need reference genome, it only does need reference transcriptome.

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8.5 years ago

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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can not open the link

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