User: Nitro_Shade

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Nitro_Shade20
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Posts by Nitro_Shade

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Which Ensembl protein id (ENSP) should I use? (Which id is used by string-db)
... Hey! Not sure if it's still relevant or not, but I made a very small utility to do this extraction. It can be found [here][1]. [1]: https://github.com/ShashwatDNagar/mapping-STRING-to-GeneSymbol ...
written 3.2 years ago by Nitro_Shade20
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Answer: A: Getting haplotype specific FASTA files from VCF files
... A solution that worked for me: I used vcf-consensus (from VCFtools) to generate the variant FASTA sequence. The Haplotype can be specified using the `-H` parameter (as 1 or 2). The resulting FASTA file can be then used to extract the gene of interest. ...
written 3.9 years ago by Nitro_Shade20
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Comment: C: Getting haplotype specific FASTA files from VCF files
... Right! I'll try this out and post my findings here. Thanks a bunch! ...
written 3.9 years ago by Nitro_Shade20
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Comment: C: Getting haplotype specific FASTA files from VCF files
... Thank you for replying. I am looking for FASTA files for both chromosomes (listed as 0|1 etc. in the VCF file) - and the tool only gives me one. The intervals tools is actually really helpful and I am using it to extract my gene of interest from the reference sequence. Thanks again! I would appr ...
written 3.9 years ago by Nitro_Shade20
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Comment: C: Getting haplotype specific FASTA files from VCF files
... I was thinking of an awk statement to split all the file with the same GT information (1|0, 0|1). Like: awk 'BEGIN{OFS="\t"} {if($1 ~ /^#/ || $10 == "0\|1" || $10 == "1\|1"){print;}}' input_VCF_file > output_1.vcf awk 'BEGIN{OFS="\t"} {if($1 ~ /^#/ || $10 == "1\|0" || $10 == "1\|1"){pri ...
written 3.9 years ago by Nitro_Shade20
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Comment: C: Getting haplotype specific FASTA files from VCF files
... Thank you for your detailed reply. Yes, I had the same terminology for phasing in mind - but this makes it far clearer. Thanks! As for my problem statement - I want to get altered FASTA files (like haplotypeA.fasta and haplotypeB.fasta from your example) and I have a VCF file and a reference seque ...
written 3.9 years ago by Nitro_Shade20
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Comment: C: Getting haplotype specific FASTA files from VCF files
... The VCF file I have are phased (they have information about the presence/absence of the SNP in either of the chromosomes). I may be wrong here or may have used incorrect terminology - I'm new to this sort of analysis and am hence asking for help. Any help is greatly appreciated. ...
written 3.9 years ago by Nitro_Shade20
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Getting haplotype specific FASTA files from VCF files
... I have been trying to get FASTA (with altered nucleotide sequences) sequences from VCF file. I have tried using FastaAlternateReferenceMaker (from GATK) but it only gives me a single FASTA file. Any help will be greatly appreciated. Thank you! ...
genome snp written 3.9 years ago by Nitro_Shade20
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Comment: C: Comparing two gene lists for orthologs
... Thanks! I'll try it out. ...
written 4.3 years ago by Nitro_Shade20
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Comment: C: Comparing two gene lists for orthologs
... They don't. That's why I need to access orthologs :) ...
written 4.3 years ago by Nitro_Shade20

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Popular Question 3.2 years ago, created a question with more than 1,000 views. For Getting haplotype specific FASTA files from VCF files

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