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2 hours ago by


You seem to have genomic coordinates in there like 21:43519790:43519815.

You can extract them with awk into featureCount SAF format (see manual for details):

awk '{if($1 ~ /^>/) print}' test.txt 
| awk -F "sapiens:" '{print $2}' 
| awk -F ":" 'OFS="t" {print $1"_"$2"_"$3, $1, $2, $3, $4}' 
| awk '{gsub("Plus","+");gsub("Minus","-");print}' > test.saf

Then use featureCounts to quantify bam files against that SAF file:

featureCounts -a test.saf -F SAF -o test_countmatrix.saf *.bam

Be sure though that the chromosome names in BAM and SAF have the same naming convention, so both are called e.g. 1 for chromosome one and not like 1 in the SAF and chr1 in the BAM.


modified 2 hours ago

2 hours ago


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