User: Cindy

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Cindy0
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Posts by Cindy

<prev • 19 results • page 1 of 2 • next >
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Comment: C: MToolBox mapExome.py error
... I tried to disable "if not os.path.exists(folder): os.mkdir(folder)" in mapExome.py, line 66. Then the script can go through, but no reads assembled.My guess is the issue is in mapExome.py. But I don't know how to fix it. #!/usr/bin/python """ Written by Ernesto Picardi - e.picard ...
written 20 days ago by Cindy0 • updated 20 days ago by genomax29k
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MToolBox mapExome.py error
... I am using MToolBox to analysis mtDNA NGS data. When it runs mapExome.py for alignment, always showing error: EXECUTING READ MAPPING WITH MAPEXOME... mapExome for sample F-00-02-44707, files found: F-00-02-44707.fastq F-00-02-44707.R1.fastq F-00-02-44707.R2.fastq F-00-02-44707.fast ...
alignment sequencing written 20 days ago by Cindy0 • updated 20 days ago by genomax29k
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Comment: C: MToolBox.sh: line 173: check_files.py: command not found
... Yes. It is. GATK and SamToFastq.jar are in the same folder (ext_tools). fastq files have been successfully generated. But IndelRealigner command not found. ...
written 27 days ago by Cindy0
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Comment: C: MToolBox.sh: line 173: check_files.py: command not found
... After a couple of hours running, it showed another error: IndelRealigner command not found. I have already cp theGenomeAnalysisTK.jar to MToolBox/ext_tools. Any idea? Thanks ...
written 27 days ago by Cindy0
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Comment: C: Compare BAM files
... Yes, I need to install other programs. It works now. Thanks ...
written 27 days ago by Cindy0
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Answer: A: MToolBox.sh: line 173: check_files.py: command not found
... Yes. It works now. I am so stupid, I did't know the PATH is the issue since I cd to the MToolBox folder. Thanks! ...
written 27 days ago by Cindy0
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Compare BAM files
... I want to compare two bam files to see whether they are same, how many reads they overlapped, and how many reads are unique. bam1 file was got several years ago and then I convert it to bam1_r1_fq and bam1_r2_fq and then remap to the new reference genome and got new sam file. Then I sorted, added he ...
sequencing written 27 days ago by Cindy0 • updated 27 days ago by genomax29k
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MToolBox.sh: line 173: check_files.py: command not found
... Anyone use MToolBox to analysis mtDNA sequencing data? When I run MToolBox, it always shows this error. "bash MToolBox.sh -i config.sh setup.sh file not found. Setting MToolBox environment sourcing conf.sh file setting up MToolBox variables in config file ... ...done Check python version... (2.7 r ...
sequencing written 28 days ago by Cindy0
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IndelRealign mitochondrial DNA using b37
... I want to run GATK IndelRealigner for mtDNA and use b37 indel reference as known sites. Here is my script. I got error for incompatible contigs. The NC_012920.1.fasta is mitochondria reference genome and includes only M contigs. How can I modify it to make it compatible to b37 indel reference genome ...
alignment written 29 days ago by Cindy0 • updated 29 days ago by genomax29k
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Answer: A: Picard tools samtofastq for a folder
... That's my final code and it works. First, use SamToFastq to generate *_R1_fq.gz and *_R2_fq.gz, then use mkdir and mv to move all fastq files to a new folder. find /path/to/folder/ -name "*.bam" | while read F ; do java -jar picard.jar SamToFastq \ INPUT=$F \ ...
written 4 weeks ago by Cindy0 • updated 4 weeks ago by genomax29k

Latest awards to Cindy

Scholar 27 days ago, created an answer that has been accepted. For A: MToolBox.sh: line 173: check_files.py: command not found

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