Question: Converting from BED to SAF/GFF
gravatar for ccag
2.9 years ago by
Boston, MA
ccag30 wrote:

I called peaks using MACS2 and now would like to use my narrowPeak file to do featureCounts. As far as I can tell, featureCOunts only uses SAF or GFF formats. Does anyone know an easy way to convert between a bed and these file types for Dm3?

featurecount gff bed saf • 3.7k views
ADD COMMENTlink modified 17 months ago by ATpoint26k • written 2.9 years ago by ccag30
gravatar for ATpoint
17 months ago by
ATpoint26k wrote:
awk 'OFS="\t" {print $1"."$2+1"."$3, $1, $2+1, $3, "."}' in.narrowPeak > out.saf

The +1 on $2 because narrowPeak is 0-based, but SAF is 1-based. $1 is the GeneID, I typically use a simple concat of the genomic coordinates, and $5 is just "." because MACS peaks are not strand-specific.

ADD COMMENTlink modified 17 months ago • written 17 months ago by ATpoint26k

Thanks for the code.

According to the manual of Rsubread. The SAF file should also include a header line, otherwise featureCounts would terminate with the error "ERROR: no features were loaded in format SAF.".

awk 'BEGIN{FS=OFS="\t"; print "GeneID\tChr\tStart\tEnd\tStrand"}{print $4, $1, $2+1, $3, "."}' ${sample}_peaks.narrowPeak > ${sample}_peaks.saf
ADD REPLYlink written 8 months ago by niuyw30
gravatar for Jeffin Rockey
2.9 years ago by
Jeffin Rockey1.1k
Jeffin Rockey1.1k wrote:

Option 1 :GenomeTools

Option 2: Go to galaxy oqtans page here and on the left pane there is "GFF Toolkit" which has BED_to_GFF3 converter .

Option 3: A long route. From here make use of bedToGenePred followed by genePredToGtf to get a gtf file at first. Then you can make use of the lot of tools that does a gtf to gff3 conversion.

I am mentioning multiple options because depending on whether you bed file is 6 column or 12 column or so, some may not be applicable.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Jeffin Rockey1.1k
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