Extract Genomic DNA tool behavior

Question: Extract Genomic DNA tool behavior

8 months ago by

Hi I have downloaded RNA_seq data as fastq files and aligned these against FASTA sequences as references, then generated GTF files. However, the coordinates of the transcripts, given by cufflinks, do not match with the length of the output sequences generated by the Extract Genomic DNA tool - these sequences, which represent repeated stretches, seem to be nearly perfect duplications of the sequences predicted by cufflinks. My question is if one can trust that the Extract Genomic DNA tool correctly output assembled sequences when it comes to repeated sequences.

Vidar

fasta genome gtf cufflinks extract • 279 views

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modified 7 months ago • written 8 months ago by vidar.blikstad • 0

7 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool extracts genomic sequence based on the coordinates. One fasta sequence per input line (bed, gtf). Repeats are soft-masked for most genomes indexed at https://usegalaxy.org and can be extracted.

If the coordinates are provided in GTF format or BED12, then the result will be spliced fasta output. This is different than the start/end coordinates of GTF lines labeled as "transcripts" -- those coordinates include the total genomic span, exons plus introns plus possibly 5'/3' UTR.

And if you are trying to compare a public annotation GTF with a Cufflinks GTF result, differences are expected, as Cufflinks generates transcripts based on the actual reads given as input, and may contain variation or novel content.

Thanks, Jen, Galaxy

ADD COMMENT • link modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson ♦ 25k

7 months ago by

vidar.blikstad • 0

vidar.blikstad • 0 wrote:

Hello

It seems clear to me now - thanks a lot

Vidar

ADD COMMENT • link written 7 months ago by vidar.blikstad • 0

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