how to edit the parameter (-d DIS Position range near start codon or stop codon)?

[shwdmsh]

Hi, If I want to get the range of -20,40 near start codon or stop codon ,how to do ? My command as follows: ribotish quality -b test.sort.bam -p 8 -l 145,151 -d 60 --nom0 -g genomic.gtf some error information:IndexError: tuple index out of range

[zhpn1024]

Try -d -20,40. Do you use the length ~150nt? It is suggested to remove adaptors before alignment.

[shwdmsh]

Hi, the test seq length is ~150nt, which is the RNA_seq data. When I use Riboseq data,the test2 seq length is about 28nt. I use the command :ribotish quality -b test.sort.bam -p 8 -d -20,40 -g genomic.gtf some error information:ribotish quality: error: argument -d: expected one argument However,I use the command : ribotish quality -b test.sort.bam -p 8 -g genomic.gtf, I can get the quality pdf file

[zhpn1024]

The problem may be that python argparse takes the minus character '-' in '-20,40' as sign of another option parameter instead of argument value. Try -d-20,40 (no space after d) or -d ' -20,40' (add quotes and another space before '-').

在 2021-03-17 10:35:08，"shwdmsh" @.***> 写道：

Hi, the test seq length is ~150nt, which is the RNA_seq data. When I use Riboseq data,the test2 seq length is about 28nt. I use the command :ribotish quality -b test.sort.bam -p 8 -d -20,40 -g genomic.gtf some error information:ribotish quality: error: argument -d: expected one argument However,I use the command : ribotish quality -b test.sort.bam -p 8 -g genomic.gtf, I can get the quality pdf file

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