Closed liyun831229 closed 6 years ago
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
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.
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 refindex
run bowtie2 assembly: _bowtie2 –x refindex -1 r1.fastq -2 r2.fastq --reorder –S PE.sam
run bPTR _bPTR -f GCF_000253395.1_ASM25339v1genomic.fna -s PE.sam -o test.tsv -plot test.pdf -m coverage -ff