I'm runnig next command
featureCounts -s 1 -t exon -g Parent -a test.gff -o test.counts test.sam
in test.sam
HWI-ST568:115:D04H3ACXX:7:1101:5518:2079 0 gi|448814763|ref|NC_000962.3| 2125761 255 61M * 0 0 TGGACAAGCTAGGAGAGGAGCTTTACTCGGCGCAGTGCGTCTCTCGCCCACCGACCTGATG CCCFFFFFHDBHHIGFHIEGHIIJCCGHHJHHJBHGHGIGGIDGGGGHGAEFFDDDDDDDD XA:i:0 MD:Z:61 NM:i:0
in test.gff
TEST GenBank exon 2125761 2504608 . - . Parent "XXX"
I get in test.counts,
# Program:featureCounts v1.5.0; Command:"featureCounts" "-s" "1" "-t" "exon" "-g" "Parent" "-a" "test.gff" "-o" "test.counts" "test.sam"
Geneid Chr Start End Strand Length test.sam
XXX TEST 2125761 2504608 - 378848 0
I expected,
# Program:featureCounts v1.5.0; Command:"featureCounts" "-s" "1" "-t" "exon" "-g" "Parent" "-a" "test.gff" "-o" "test.counts" "test.sam"
Geneid Chr Start End Strand Length test.sam
XXX TEST 2125761 2504608 - 378848 1
What's the mistake that I'm making?
•
written
by
jrbustosm •
"gi|448814763|ref|TEST|"
instead of
"gi|448814763|ref|NC_000962.3|"
?
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written
by
jrbustosm •
Just "TEST", unless you edited things to remove gi|448814763|ref|NC_000962.3| from the GFF file snippet you posted.
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written
by
Devon Ryan
thanks @Martombo, @Devon Ryan this solved my problem
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written
by
jrbustosm •
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Aside from the chromosome name issue, I imagine that the strandedness setting would cause problems as well.
You are right ..... this is the problem thanks