Hi guys,
I've just wondering if someone here know how to get the S.pombe annotation over the non-coding regions. As I am using chipseeker for the annotation:
txdb_pombe <- makeTxDbFromGFF("Schizosaccharomyces_pombe.ASM294v2.34.gff3.gz", format="gff3", organism = "Schizosaccharomyces pombe", taxonomyId = "4896")non-coding regions
fileList <- list.files( ,pattern = "*.BED")
for (i in fileList){
print(i)
peak <- readPeakFile(i, header=F)
print(peak)
peakAnno <- annotatePeak(peak, tssRegion=c(-2000, 2000), TxDb = txdb_pombe)
print(peakAnno)
write.table(peakAnno, paste("annot_total_", i, sep="") , sep="\t", col.names=T, row.names = F, quote=F)
}
As my gff3 genome only have the coding regions for S.pombre, I can't get the intron annotation. I'd would like to know if anyone know how I can get the whole annotation for S.pombe including also the non-coding regions
Thanks!
•
written
by
Lila M
2 answers
Hi !
Reference annotation of S.pombe is on pombase. Go into downloads > datasets > genome-datasets > feature coordinates (or just click here).
Note that there is one .gff3 file by chromosome, you might need to merge them.
Introns are a type of "biological regions" so you'll need to look for those lines :
chrom source feature start end a strand b c
I . biological_region 180528 180585 1 + . assembly_name=ASM294v2;external_name=SPAC13G6.04.1:intron:1;logic_name=intron
introns , 5' and 3' UTRs, ncRNAs, promoters ... they are all annotated in that file. Just search "intron" and you will see :)
So the annotation is fine, the issue now is in how ChIPseeker reads it. Sadly I can't really help here because I don't use this package. Perhaps you should ask a new question or edit the title of this one.
PS : A wild guess : ChIPseeker maybe can't parse "biological_region" features. But if you change this
chrom source feature start end a strand b c
I . biological_region 180528 180585 1 + . assembly_name=ASM294v2;external_name=SPAC13G6.04.1:intron:1;logic_name=intron
into this :
chrom source feature start end a strand b c
I . intron 180528 180585 1 + . assembly_name=ASM294v2;external_name=SPAC13G6.04.1:intron:1;logic_name=intron
it might work. or not.
> require(GenomicFeatures)
> x <- makeTxDbFromGFF("schizosaccharomyces_pombe.chr.gff3")
> sapply(intronsByTranscript(x)[1:10], length)
1 2 3 4 5 6 7 8 9 10
0 0 0 0 1 0 1 1 0 0
> intronsByTranscript(x)[5]
GRangesList object of length 1:
$5
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] I [18307, 18348] +
Indeed makeTxDbFromGFF can parse intron from this GFF file and ChIPseeker use this information to annotate your peak.
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