count mapped reads of small RNA by length and defined loci · Biostar

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count mapped reads of small RNA by length and defined loci

Hi all,

I have small RNA-seq reads mapped to Arabidopsis genome. How can I do If I want to know how many reads of 18 - 30 nt mapped to defined loci (e.g genes and TEs), respectively.

results like this: length counts 18 n 19 n 20 n . . . . . .

I have gtf files for genes and TEs Genes: 1 tair gene 3631 5899 . + . gene_id "AT1G01010"; gene_name "NAC001"; gene_source "tair"; gene_biotype "protein_coding"; 1 tair transcript 3631 5899 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1"; gene_name "NAC001"; gene_source "tair"; gene_biotype "protein_coding"; transcript_name "ANAC001"; transcript_source "tair"; transcript_biotype "protein_coding"; 1 tair exon 3631 3913 . + . gene_id "AT1G01010"; transcript_id "AT1G01010.1"; exon_number "1"; gene_name "NAC001"; gene_source "tair"; gene_biotype "protein_coding"; transcript_name "ANAC001"; transcript_source "tair"; transcript_biotype "protein_coding"; exon_id "AT1G01010.1.exon1";

TEs: 1 tair TE 15827287 15838845 . - . gene_id "AT1TE52125"; 1 tair TE 13085455 13085593 . + . gene_id "AT1TE42735"; 1 tair TE 11181821 11181959 . + . gene_id "AT1TE36140";

Thanks in advance!!

rna-seq

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written 9.8 years ago by SpreeFU •

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