problem in getting the PTR value

[liyun831229]

Hi, I am trying to use iRep in my dataset. However, the PTR value returned is N/A. Is there any problem from the command I am using?

1. I first generate the indexed reference using bowtie2 _bowtie2-build GCF_000253395.1_ASM25339v1_genomic.fna refindex

2. run bowtie2 assembly: _bowtie2 –x refindex -1 r1.fastq -2 r2.fastq --reorder –S PE.sam

3. run bPTR _bPTR -f GCF_000253395.1_ASM25339v1genomic.fna -s PE.sam -o test.tsv -plot test.pdf -m coverage -ff

[christophertbrown]

Hello,

There are several reasons why it may not be possible to determine an accurate PTR value. In these cases, 'n/a' is reported instead of a value. Usually this is due to low coverage.

I may be able to identify the cause if you send me your output.

Best,

Chris

On Aug 10, 2017, at 12:50 PM, liyun831229 notifications@github.com wrote:

Hi, I am trying to use iRep in my dataset. However, the PTR value returned is N/A. Is there any problem from the command I am using?

• I first generate the indexed reference using bowtie2 bowtie2-build GCF_000253395.1_ASM25339v1_genomic.fna ref_index

• run bowtie2 assembly: bowtie2 –x ref_index -1 r1.fastq -2 r2.fastq --reorder –S PE.sam

• run bPTR bPTR -f GCF_000253395.1_ASM25339v1_genomic.fna -s PE.sam -o test.tsv -plot test.pdf -m coverage -ff

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