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The multicov command takes a feature file (GFF) and counts how many reads are in certain regions from many input files. By default it counts how many reads overlap the feature on either strand, but it can be made specific with an the -s option. Note: Remember that the chromosome names in your gff file should match the way the chromosomes are named in the reference fasta file used in the mapping step. For example, if gff file contains chr1, chrX etc, the GFF file must also call the chromosomes as chr1, chrX and so on.
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bedtools multicov -s -bams SRR034450.bam SRR034451.bam SRR034452.bam SRR034453.bam -bed NC_017544.1.genes.gff > gene_counts.gff
head gene_counts.gff
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