Information needed in .bed file for geneBody_coverage.py

[magnus jespersen]

Hello,

I'm trying to produce a gene body coverage plot using geneBody_coverage.py. I work with a bacteria, and thus have to produce the gene model bed file myself (example attached). However I cannot get the function to produce a gene body coverage plot. 

I looked into the python code and saw that the stand and gene name was used so I added those into the .bed file, but am I missing something in the .bed file?
I'm running RseQC version 3.0.1.

Here is an example of what is printed to stdout when running:

geneBody_coverage.py -i 5448_1_HL7J5DRXX_AGCTCGCT-GCAGAATC_to_5448.sorted.bam.bai -o 5448 -r ../../References/gene_body_genes/5448_con_exp_genes.bed 

@ 2020-07-31 13:53:16: Read BED file (reference gene model) ...

@ 2020-07-31 13:53:16: Total 13 transcripts loaded

@ 2020-07-31 13:53:16: Get BAM file(s) ...

Sample Skewness

@ 2020-07-31 13:53:16: Running R script ...

null device 

          1 

[magnus jespersen]

And I have checked that the chromosome ID is the same for the .bed and .bam

example line of .bam file: A00121:248:HL7J5DRXX:2:1254:3595:12070 16 NZ_CP008776.1 62753 60 100M * 0 0 GAATTCCGTGGAAAA

[Liguo Wang]

Hello,

your bed file is not correct. please strictly follow these instructions to make BED file. 

https://genome.ucsc.edu/FAQ/FAQformat.html#format1

Thanks

Liguo

[magnus jespersen]

Thank you for the reply. I have revised my bed-file but cannot spot what you suggest is wrong. Can you point me more specifically to what you have seen? I have the 12 required fields. I have the chromosome, start, end and strand which seems to be the information used by geneBody_coverage.py, so what specifically am I missing or is wrong with the formatting?

Thanks,

Magnus

[Liguo Wang]

Standard BED file has 12 fields. The first 6 fields define the transcribed region. The last 6 fields define the starts/ends positions of exons, introns which are very important for geneBody_coverage.py. 

Did you read this: https://genome.ucsc.edu/FAQ/FAQformat.html#format1 ?

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