calculate meandepths for CDSs after mapping transcriptome reads to the genome
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4 days ago
poecile.pal ▴ 40

Good morning,

I have mapped transcriptome reads to the genome and have bam file now.

I know, how to calculate meandepth for "chromosomes", which are named in my gtf file as NODEs.

samtools coverage hisat2map.bam -o hisat2map_coverage.txt

It produces file with meandepths for chromosomes (NODEs).

#rname       ...       meandepth       ...
NODE_1       ...       9       ...
NODE_2       ...       30       ...

But each NODE has a lot of CDSs, which is specified in gtf:

NODE_1        AUGUSTUS        gene    200 300 .       -       .       jg12345
NODE_1        AUGUSTUS        transcript      .       .       .       -       .       transcript_id "jg12345.t1"; gene_id "jg12345"
NODE_1        AUGUSTUS        stop_codon      200 202 .       -       0       transcript_id "jg12345.t1"; gene_id "jg12345";
NODE_1        AUGUSTUS        CDS     200 230 0.77    -       2       transcript_id "jg12345.t1"; gene_id "jg12345";
NODE_1        AUGUSTUS        CDS     240 260 0.14    -       0       transcript_id "jg12345.t1";

So,

Question: How to calculate meandepths for CDS?

Input: bam and gtf

Output: file with meandepths for CDSs:

#name       ...       meandepth       ...
NODE_1_CDS1       ...       10       ...
NODE_1_CDS2       ...       50       ...

What I tried: cut the CDS coordinates from gtf, make a bed file out of it like

NODE_1_CDS1   200 230
NODE_1_CDS2   240 260

and give as input samtools depth after the -b flag:

samtools depth hisat2map.bam -b annotation_onlyCDS.bed -o hisat2map_depth_onlyCDS.txt

Next, I was going to average the depths by CDSs. But this command gives an empty file. I think the reason is that in the gtf file (and, accordingly, in my bed) the numbering goes through the entire genome, and in the bam file it is separate for each NODE.

Could you help me, please?

Thank you very much in advance!

Best regards, Poecile

gtf sam meandepth samtools alignment • 105 views
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