Question

Human transcriptome download

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6.7 years ago

KVC_bioinfo ▴ 590

Hello,

I am going to align the RNA -seq data to human transcriptome. However, I am not sure which database I should use. NCBI's RefSeq or RefSeqGene or anything else?

Can anyone help me with that?

Thank you in advance

RNA-Seq transcriptome • 8.5k views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 6.7 years ago by KVC_bioinfo ▴ 590

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You should use the whole genome for alignment and then use a GFF file to do your counting.

ADD REPLY • link 6.7 years ago by GenoMax 142k

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We plan to use Human transcriptome. I will also need the gtf file for that. from where I can get that?

ADD REPLY • link 6.7 years ago by KVC_bioinfo ▴ 590

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While you could get that data from multiple places, Illumina has bundles that contains matched sequence, annotation and index files for bowtie2/bwa hosted at iGenomes site for many genomes, including human.

ADD REPLY • link 6.7 years ago by GenoMax 142k

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Yes. But it is human genomes. I am looking to download Human transcriptome.

ADD REPLY • link 6.7 years ago by KVC_bioinfo ▴ 590

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If you are referring to a set of transcript sequences (minus the introns/non-coding regions) then Ensembl Human Genome page is as a good place as any. Look under "gene annotation" on right side.

ADD REPLY • link 6.7 years ago by GenoMax 142k

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II found this

And from that page, i downloaded RefSeq Transcripts. Is it correct? Also, I need annotation file when aligning with STAR. Could you please tell me how do I get that? thank you very much.

ADD REPLY • link 6.7 years ago by KVC_bioinfo ▴ 590

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Make this easy on yourself. Follow the directions to get pre-made indexes for STAR: C: Pre made STAR Index?

ADD REPLY • link 6.7 years ago by GenoMax 142k

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I looked into it. it does not have a pre made an index for human transcriptome

ADD REPLY • link 6.7 years ago by KVC_bioinfo ▴ 590

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Have you looked at STAR manual? It may be good to spend some time and go through it.

ADD REPLY • link 6.7 years ago by GenoMax 142k

score 3 · Answer 1 · 2017-11-01

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6.5 years ago

Kevin Blighe 87k

Just use GENCODE's reference transcriptome FASTA:

https://www.gencodegenes.org/releases/current.html

[Direct link to gzipped FASTA: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.transcripts.fa.gz]

I have done this for hundreds of RNA-seq samples

ADD COMMENT • link 6.5 years ago by Kevin Blighe 87k

score 2 · Answer 2 · 2017-08-31

I recommend you to use the information available in the Table Browser from UCSC. Pick your genome version (hg19 or hg38), choose your annotations (Ensembl, RefSeq, etc.) and get the GTF output format. RefSeq is a good starting point. If you need a transcriptome fasta file, you can use the gtf_to_fasta tool available in the TopHat2 package. You will be able to use this file with many aligners (not restraint to TopHat2).