User: pfs

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pfs200
Reputation:
200
Status:
Trusted
Location:
USA/Boston
Last seen:
12 hours ago
Joined:
5 months ago
Email:
f***************@gmail.com

Posts by pfs

<prev • 40 results • page 1 of 4 • next >
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Answer: A: finding function of genes from their coordinates
... I would start here https://www.ncbi.nlm.nih.gov/protein/. If you have a manhattan plot of SNPs then you may want to annotate the SNPs using an annotation program such ANNOVAR to determine the what your SNP may actually be effecting. ...
written 1 day ago by pfs200
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Answer: A: Merging data coloum wise in R
... Look into the merge command. ...
written 6 days ago by pfs200
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Comment: C: Samtools mpileup ends abruptly without completing full analysis
... Default mpileup will only output variants. Are you anticipating variants in all your bam files? ...
written 21 days ago by pfs200
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Comment: C: Given QTLs and genome annotation, quickly list genes closest to QTLs
... I do not have first hand experience doing this but the 'Experimental Design' section in 'Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR' should get you started. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718734/ ...
written 29 days ago by pfs200
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Comment: C: how to annotate chromosome position with the gene list file
... This looks like a bedtools intersect problem. What command did you use? ...
written 29 days ago by pfs200
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Answer: A: Suggestions regarding bioinformatics journal
... I would post the article on a non-peer reviewed site first so you get your work out there and claim the space. See https://www.biorxiv.org/. In your situation I would just submit the article to another journal. ...
written 29 days ago by pfs200
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Answer: A: SNPSVM - not able to find VCF file
... Have you told SNPSVM where libsvm is? See installation step 3. https://github.com/brendanofallon/SNPSVM ...
written 4 weeks ago by pfs200
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Answer: A: Given QTLs and genome annotation, quickly list genes closest to QTLs
... Have you looked into ANNOVAR? ...
written 5 weeks ago by pfs200
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Answer: A: SNPSVM - not able to find VCF file
... Is the vcf file located in the directory you are trying to execute the program? If not go back and include the path after the -V argument. ...
written 5 weeks ago by pfs200
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Answer: A: SNP calling from a scaffold.fa file
... Is this what you are looking for? http://sjackman.ca/abyss-activity/ ...
written 6 weeks ago by pfs200

Latest awards to pfs

Teacher 29 days ago, created an answer with at least 3 up-votes. For A: How to find the unique list of mismatches of reads with the reference genome
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to find the unique list of mismatches of reads with the reference genome
Scholar 11 weeks ago, created an answer that has been accepted. For A: How to find the unique list of mismatches of reads with the reference genome
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How to find the unique list of mismatches of reads with the reference genome
Scholar 3 months ago, created an answer that has been accepted. For A: How to find the unique list of mismatches of reads with the reference genome
Scholar 3 months ago, created an answer that has been accepted. For A: How to find the unique list of mismatches of reads with the reference genome
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to find the unique list of mismatches of reads with the reference genome

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