Subread FeatureCounts produces zero percent successfull alignment
Dear All, I working on rice genome transcriptome analysis. I have done alignment using the Hisat2 tool process greater than 80% s score. Then I perform the count matrix generation using the subread package
Commad Subread
/apps/subread-1.6.2-source/bin/featureCounts -p -B -a all.gtf -o counts *bam
Reference fasta file
>LOC_Os01g01010 genomic|TBC domain containing protein, expressed
AGATGAGCTGGTGGGGATGCTCTAAGAGAACGAGAGAAGCACAGAGCAGATAAACCACAC
CCACAGGCACCACCGTCCTTGTTGGTAATGAAGAAGACGAGACGACGACTTCCCCACTAG
GAAACACGACGGAGGCGGAGATGATCGACGGCGGAGAGAGCTACAGAAACATCGATGCCT
CCTGTCCAATCCCCCCATCCCATTCGGTAGTTGGATTGAAGACTACCGAATAAGAGAAGC
GTF file all.gtf
Chr1 MSU_osa1r7 exon 2903 3268 . + . transcript_id "LOC_Os01g01010.1"; gene_id "LOC_Os01g01010"; gene_name "LOC_Os01g01010";
Chr1 MSU_osa1r7 exon 3354 3616 . + . transcript_id "LOC_Os01g01010.1"; gene_id "LOC_Os01g01010"; gene_name "LOC_Os01g01010";
Chr1 MSU_osa1r7 exon 4357 4455 . + . transcript_id "LOC_Os01g01010.1"; gene_id "LOC_Os01g01010";gene_name "LOC_Os01g01010";
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Carlo Yague
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mathavanbioinfo
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mathavanbioinfo
1 answer
As you can see in your files the FASTA file does not match the GFT file
Now how you reference file calls the sequences >LOC_Os01g01010 whereas the feature file designates them as Chr1
Make sure to use a genomic file, not a transcriptome file as your alignment target.
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Istvan Albert
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