User: nbhassou

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nbhassou10
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New User
Location:
United States
Last seen:
2 years, 1 month ago
Joined:
2 years, 2 months ago
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Posts by nbhassou

<prev • 8 results • page 1 of 1 • next >
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Answer: A: VCF gene name sorting
... Hello,   This is an example of what I am getting:  fileformat=VCFv4.1 ##fileDate=20151018 ##source=freeBayes v0.9.20 ##reference=/galaxy/data/hg19/sam_index/hg19.fa ##phasing=none ##commandline="freebayes --bam localbam_0.bam --fasta-reference /galaxy/data/hg19/sam_index/hg19.fa --vcf /galaxy-rep ...
written 2.1 years ago by nbhassou10
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VCF gene name sorting
... Hello, I have a vcf file and need to tie it to the gene name. I did this with the vcf annotate tool using the hg19 genome as the BED file. The gene name is in the info field of the vcf file. But now I need to find the gene with the most polymorphisms. I don't know how to do this without delimiting ...
vcf gene name written 2.1 years ago by nbhassou10
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Answer: A: Filtering on tabular dataset from vcf
... Hey, yeah the vcf filter isn't as intuitive. I feel your pain- I wanted to bring it to excel to figure out how to sort, but finally figured it out. You should definitely provide feedback for the course when evals come around. I felt a little in the dark too. Hopefully the project I submit is correct ...
written 2.1 years ago by nbhassou10
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Answer: A: Filtering on tabular dataset from vcf
... Hi judyh,  I first had to tab delimit the vcf file. Then I actually filtered with the regular filter tool. To find lines with mnp, for example, I used the select option instead of filter option. I couldn't figure out the VCF filter tool actually, sadly enough.  ...
written 2.1 years ago by nbhassou10
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Filtering on tabular dataset from vcf
... Hello, I tab delimited a vcf file so that I could filter on the 'type' information, which was included in a series of information separated by semicolons. I now want to filter for lines that contain 'TYPE=snp'. Some of the types includes 'TYPE=snp, del', or another combination of types of variants. ...
filter string vcf written 2.2 years ago by nbhassou10 • updated 2.1 years ago by judyh0
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Answer: A: Having issues uploading files into Galaxy
... Interestingly it worked this morning, although I did the exact same thing.  ...
written 2.2 years ago by nbhassou10
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Comment: C: Having issues uploading files into Galaxy
... Hi Jennifer, The files each are less than 500 mb. They are uncompressed, and all are .fastq files. Not sure what else I can try? ...
written 2.2 years ago by nbhassou10
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Having issues uploading files into Galaxy
... I am having issues uploading  FASTQ data files f into Galaxy (usegalaxy.org). I get "tool error An error occurred with this dataset: failure preparing job"  What am I doing wrong?   Thanks! ...
upload failure preparing job written 2.2 years ago by nbhassou10

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