User: vctrm67

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vctrm670
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Posts by vctrm67

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Comment: C: SNPEff missing annotations from VCF?
... 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 vctrm670
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SNPEff missing annotations from VCF?
... 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 ...
vcf snpeff written 27 days ago by vctrm670
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Comment: 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 vctrm670
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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 vctrm670
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Comment: 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 vctrm670
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Comment: 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 vctrm670
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Comment: 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 vctrm670
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Bowtie2 simple alignment errors?
... 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 ...
bowtie2 alignment bowtie written 5 weeks ago by vctrm670 • updated 5 weeks ago by h.mon27k

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