RNA-seq~featureCounts

featureCounts by subread

input_1:BAM files (unsorted bam is recommended)

input_1/SRR4425244_1.fastq.bam

input_1/SRR4425245_1.fastq.bam

input_1/SRR4425248_1.fastq.bam

input_1/SRR4425249_1.fastq.bam

input_1/SRR4425250_1.fastq.bam

input_1/SRR4425251_1.fastq.bam

input_2:GTF

input_2/Bomo_gene_models.withnote.plus.NC_002355.gtf

NC_002355.1	stdin	transcript	15095	15883	.	+	.	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1";  gene_name "gene-COX3";
NC_002355.1	stdin	exon	15095	15883	.	+	.	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "gene-COX3";
NC_002355.1	stdin	CDS	15095	15880	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "gene-COX3";
NC_002355.1	stdin	start_codon	15095	15097	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "gene-COX3";
NC_002355.1	stdin	stop_codon	15881	15883	.	+	0	gene_id "gene-COX3"; transcript_id "cds-NP_059480_1"; exon_number "1"; exon_id "cds-NP_059480_1.1"; gene_name "gene-COX3";
NC_002355.1	stdin	transcript	14403	15080	.	+	.	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1";  gene_name "gene-ATP6";
NC_002355.1	stdin	exon	14403	15080	.	+	.	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "gene-ATP6";
NC_002355.1	stdin	CDS	14403	15077	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "gene-ATP6";
NC_002355.1	stdin	start_codon	14403	14405	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "gene-ATP6";
NC_002355.1	stdin	stop_codon	15078	15080	.	+	0	gene_id "gene-ATP6"; transcript_id "cds-NP_059479_1"; exon_number "1"; exon_id "cds-NP_059479_1.1"; gene_name "gene-ATP6";

Option

-c "8" -m "64" -f "-p -t exon -g gene_id"

Output

count.id.forDEGanalysis.txt

Geneid	SRR4425244_1.fastq.bam	SRR4425245_1.fastq.bam	SRR4425248_1.fastq.bam	SRR4425249_1.fastq.bam	SRR4425250_1.fastq.bam	SRR4425251_1.fastq.bam
gene-COX3	283	426	666	368	128	123
gene-ATP6	94	192	383	179	39	46
gene-ATP8	0	0	2	1	0	0
rna-NC_002355_1_14180__14247	0	0	0	0	0	0
rna-NC_002355_1_14111__14181	0	0	0	0	0	0
gene-COX2	139	229	283	165	97	113
rna-NC_002355_1_13362__13428	1	1	0	0	0	1
gene-COX1	517	745	1370	727	385	356
rna-NC_002355_1_11752__11813	0	0	0	0	0	0

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