User: ramesh.8v

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ramesh.8v200
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Posts by ramesh.8v

<prev • 44 results • page 1 of 5 • next >
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Comment: C: Filter sam/bam files
... Thanks! It worked :) ...
written 12 months ago by ramesh.8v200
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Comment: C: Filter sam/bam files
... Thanks for the suggestion! Yes, they were mapped separately. I will look into BBTools. ...
written 12 months ago by ramesh.8v200
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Filter sam/bam files
... Hi: I mapped single-end sequenced GBS reads onto two similar genomes. I have two sam files one for each genome. I'm interested to filter sam/bam files based on these conditions: 1. reads unique to a genome/reads mapped only on one genome 2. reads are not unique/mapped on both genomes. Are there ...
filter bam samtools sam gbs written 12 months ago by ramesh.8v200 • updated 12 months ago by swbarnes25.8k
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Comment: C: how to find genes based on SNP rsIDs
... In addition to Ram's suggestion, if you know flanking sequences, just do NCBI BLAST search. ...
written 18 months ago by ramesh.8v200
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Comment: C: allelic phylogenic clustrering or tree
... Try Darwin program (http://darwin.cirad.fr/). It accepts allelic data and they made a very nice tutorial. ...
written 18 months ago by ramesh.8v200
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Comment: C: How to command python to continue beyond the loop?
... What you mean "End of the list"? Do you mean, the last element of the list? If yes, grab the last element by result[-1] ...
written 18 months ago by ramesh.8v200
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Answer: A: Transform duplicate rows into columns.
... A quick python3 solution: make sure your input file is tab-separated out = {} with open("input.txt") as f: for lines in f: lines = lines.strip().split("\t") if lines[0] not in out: out[lines[0]] = [set(), set(), set(), set(), set(), set()] ...
written 18 months ago by ramesh.8v200
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Comment: C: How to differentiate Homozygous reference calls from No calls in VCF
... Thanks, Brain. That's a very good idea. But, raw read depth is not printed for individual samples, how to force bcftools to print raw read depth? ...
written 2.5 years ago by ramesh.8v200
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How to differentiate Homozygous reference calls from No calls in VCF
... I'm using samtools multisample SNP calling to call SNPs from different samples. The command I'm using is, samtools mpileup -uf ref.fa *.bam | bcftools view -vcg - > out.vcf Then, I'm using vcf-to-tab tool to convert vcf to tab file. The problem is, No calls (missed in sequencing) are calle ...
snps samtools written 2.5 years ago by ramesh.8v200 • updated 2.5 years ago by genomax68k
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How to call heterozygous SNPs
... We sequenced and assembled a genome. Now, I'm interested to call all heterozygous SNPs of the same genome. For that, I mapped paired end reads (same reads used for the genome assembly) back to the same genome. Is there a pipeline to call these heterozygous SNPs? I appreciate any sort of help. ...
gatk next-gen samtools snp written 2.5 years ago by ramesh.8v200

Latest awards to ramesh.8v

Popular Question 9 months ago, created a question with more than 1,000 views. For Patchy alignment in bowtie
Popular Question 18 months ago, created a question with more than 1,000 views. For How/where to download Human recombination map/hotspots?
Popular Question 18 months ago, created a question with more than 1,000 views. For Parse mapped scaffolds in BWA alignment
Popular Question 18 months ago, created a question with more than 1,000 views. For High Scoring Pairs (HSP) in BLAST output
Scholar 18 months ago, created an answer that has been accepted. For A: Parsing GLOBPROT flat text file format
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Transform duplicate rows into columns.
Popular Question 19 months ago, created a question with more than 1,000 views. For High Scoring Pairs (HSP) in BLAST output
Popular Question 2.0 years ago, created a question with more than 1,000 views. For bio::db::sam installation error
Popular Question 2.0 years ago, created a question with more than 1,000 views. For High Scoring Pairs (HSP) in BLAST output
Popular Question 2.0 years ago, created a question with more than 1,000 views. For bio::db::sam installation error
Supporter 2.7 years ago, voted at least 25 times.
Scholar 2.8 years ago, created an answer that has been accepted. For A: Parsing GLOBPROT flat text file format
Scholar 2.8 years ago, created an answer that has been accepted. For A: Parsing GLOBPROT flat text file format
Popular Question 4.0 years ago, created a question with more than 1,000 views. For how to trim multiple sequence alignmnet and de-aling the sequences?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Velvet: Segmentation fault (core dumped)

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