Multiple entries in a some columns on FeatureCounts output

Question

[myoui3122010]

Performed alignment with Bowtie2 using

bowtie2 -p 4 -x ~/shared/NGS/P4/genome/bowtie2_ind/      bowtie2_ind -1 /mnt/shared/NGS/P4/control/SRR30712601_1.fastq.gz -2 /mnt/shared/NGS/P4/control/SRR30712601_2.fastq.gz -S aligned_SRR30712601.sam

Sam to Bam using

samtools view -bS results/aligned_SRR30712601.sam -o results/aligned_SRR30712601.sorted.bam

samtools sort results/aligned_SRR30712601.sorted.bam -o results/aligned_aligned_SRR30712601.sorted.bam

samtools index results/aligned_aligned_SRR30712601.sorted.bam 

Then featureCounts was run using

 featureCounts -a ~/shared/NGS/P4/genome/Homo_sapiens.GRCh38.108.gtf \ 

-o aligned_SRR30712601_counts.txt \

-T 4 \

-p \

aligned_aligned_SRR30712601.sorted.bam 

This .txt file has multiple entries in the same rows in chr, start, end columns.

Is this normal? Can I just calculate TPM, FPKM or RPKM ?

Answer 1

[biofalconch]

Yes, this is normal as the output contains the chromosome, start and end positions for all exons. But you can just take the first and seventh (last) column which contain the Gene ID and its respective counts :) You can also take the 6th column (Length) to calculate FPKM as well.