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mgymrek / pybamview

Browser based application for viewing bam alignments
MIT License
56 stars 17 forks source link

I have a problem using pybamview. #51

Open kds135 opened 7 years ago

kds135 commented 7 years ago

Hi, My name is Kim Dong Seok who is the university student of South Korea. Nowadays I am studying RNA-Seq in my laboratory. I wanted to visualize my RNA mapping result, so I had searched some tools which can visualize the mapping result. Fortunately, I found the cool visualization tool, Pybamview! I really really want to use this tool.

Before, I use this tool, I prepared the data need to pybamview. I have a reference FASTA file and sequencing FASTQ files.

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Before I start to use pybamview, I followed stages needed to use pybamview.

First, I aligned the RNA-Seq reads to reference FASTA file by using Tophat.

the command is;

tophat -p 10 Gracilariopsis_genome.fasta Gpch_RNA_1_Idx1_ATCACG_L008_R1_001.fastq ...(ellipsis)...I put all fastq in this command. Then, I followed your pybamview step.

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And then, I got the results like this. 4

but when I run the result, I got abnormal result.

5 I don't know why the result is. I checked the result whether the data is mapped or not like this.

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I think the mapping result is correct, but why the error message is happened, whenever I use pybamview --bam acceepted_hits.sorted,bam ???

I cannot understand the error message, ERROR: No samples found in BAM file.

plead help me..

kds135 commented 7 years ago

My email address is dongseokkim6662@gmail.com help me plz...

kds135 commented 7 years ago

tophat -p 10 Gracilariopsis_genome.fasta ----> not fasta file, but index file.. (changed, it's my mistake)