User: vctrm67
vctrm67 • 0
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Posts by vctrm67
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... It is simply an SnpEff annotated VCF file that ends with .vcf.snpeff.
Alternatively, are there any tools that convert SnpEff files to BedPE files? ...
written 26 days ago by
vctrm67 • 0
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... I have an annotated VCF file (in SNPEff format). I noticed that the SNPEff format does not provide information regarding the SVType in the INFO section, whereas the VCF format does. Is there a way to recover this information?
For background, I am trying to convert vcf.snpeff file to a bedpe file u ...
written 27 days ago by
vctrm67 • 0
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C: Bowtie2 simple alignment errors?
... This is not the same index that I used in the previous script. Previously, I used a premade script from some one else; here, I am just making my own separately. ...
written 5 weeks ago by
vctrm67 • 0
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Comment:
C: Bowtie2 simple alignment errors?
... module load gcc/6.2.0
module load bowtie2/2.3.4.3
bowtie2-build -f '/path/referenceGenomes/hg19_ucsc.fa' 'hg19_ucsc' ...
written 5 weeks ago by
vctrm67 • 0
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C: Bowtie2 simple alignment errors?
... Yes. And I do have write access, as I built a bowtie2 index in the same directory using another script. ...
written 5 weeks ago by
vctrm67 • 0
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C: Bowtie2 simple alignment errors?
... I will double check, but here is the list of errors I am recieving now:
Line 14: /path/to/index/hg19_bt2: No such file or directory
Line 15: /path/to/read1.fastq.gz: cannot execute binary file
Line 16: /path/to/read2.fastq.gz: cannot execute binary file
(ERR): "-S" doe ...
written 5 weeks ago by
vctrm67 • 0
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C: Bowtie2 simple alignment errors?
... I see, thank you. So I should have instead this?
index_path='/path/to/index/hg19_bt2'
read_path_1='path/to/read1.fastq.gz'
read_path_2='/path/to/read2.fastq.gz'
module load gcc/6.2.0
module load bowtie2/2.3.4.3
bowtie2 -x $index_path -1 $read_path_1 -2 $read_path_2 -S b ...
written 5 weeks ago by
vctrm67 • 0
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... I'm new to Bowtie2 and have been trying to run some simple alignments in Bowtie2. My current bash script looks like this:
index_path= '/path/to/index/hg19_bt2'
read_path_1= 'path/to/read1.fastq.gz'
read_path_2= '/path/to/read2.fastq.gz'
module load gcc/6.2.0
module load bo ...
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