Thanks for your reply.
I am sorry, I was not clear. I mean, why only rRNA genes are considered for mitochondrial chromosome? I expected to find all the coding genes (MT-ND1, MT-ND2 ..., MT-ATP6... and so on)
Maria Angela
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I was trying to use read_distribution.py get an error, I downloaded the gtf files from UCSC and converted to bed using gtf2bed. Can you please help me.
processing /projects/ccs/schurerlab/Rimpi/Genomes/UsedForSTAR/hg38.ensGene.bed ... Traceback (most recent call last):
File "/usr/local/bin/read_distribution.py", line 302, in <module>
main()
File "/usr/local/bin/read_distribution.py", line 191, in main
intergenic_down1kb_base,intergenic_down5kb_base,intergenic_down10kb_base) = process_gene_model(options.ref_gene_model)
File "/usr/local/bin/read_distribution.py", line 75, in process_gene_model
utr_3 = obj.getUTR(utr=3)
File "/usr/local/lib/python3.6/site-packages/qcmodule/BED.py", line 433, in getUTR
cdsStart=int(fields[6])
ValueError: invalid literal for int() with base 10: 'ensGene'</module>
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Hi Maria,
I just downloaded hg19_RefSeq.bed.gz, it contains 63169 transcripts (i.e the whole transcriptome).
https://sourceforge.net/projects/rseqc/files/BED/Human_Homo_sapiens/hg19_RefSeq.bed.gz/download
Thanks for your reply.
I am sorry, I was not clear. I mean, why only rRNA genes are considered for mitochondrial chromosome? I expected to find all the coding genes (MT-ND1, MT-ND2 ..., MT-ATP6... and so on)
Maria Angela
HI Maria,
The bed file was downloaded from UCSC table browser, I have no idea why only rRNA genes were included for chrM.
Hi Maria,
I was trying to use read_distribution.py get an error, I downloaded the gtf files from UCSC and converted to bed using gtf2bed. Can you please help me.
processing /projects/ccs/schurerlab/Rimpi/Genomes/UsedForSTAR/hg38.ensGene.bed ... Traceback (most recent call last):
File "/usr/local/bin/read_distribution.py", line 302, in <module>
main()
File "/usr/local/bin/read_distribution.py", line 191, in main
intergenic_down1kb_base,intergenic_down5kb_base,intergenic_down10kb_base) = process_gene_model(options.ref_gene_model)
File "/usr/local/bin/read_distribution.py", line 75, in process_gene_model
utr_3 = obj.getUTR(utr=3)
File "/usr/local/lib/python3.6/site-packages/qcmodule/BED.py", line 433, in getUTR
cdsStart=int(fields[6])
ValueError: invalid literal for int() with base 10: 'ensGene'</module>
Hi Rimpi,
I'm experiencing the same issue that you're having as well - were you ever able to find a fix or does anyone else have some recommendations?
Not sure which GTF2BED you were using. You can either download BED file directly from UCSC table browser or convert the GTF to BED using https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html