how to extract and match information of two filein R
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@ccbf0270
Last seen 6 weeks ago
italy

Hi i have two file, the first one is the list of genes ID and the second one is a GTF file. i want to extract information of chr,start,end,gene_id,strand from the second file in R

-first file:
 gene_id
 LOC124418406
 LOC1211106832
 ......
-second file (gtf) is as attached image.

enter image description here

 - i want the out put as below:
 chr(seqname)  Feature Start  End  gene_id  Strand
.....

```

R column match • 760 views
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@james-w-macdonald-5106
Last seen 8 hours ago
United States
> library(rtracklayer)
> library(GenomicFeatures)
> txdb <- makeTxDbFromGFF(<your gff filename goes here>)
> genes(txdb)

There are vignettes for both rtracklayer and GenomicFeatures.

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thank you!

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