User: merodev

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merodev140
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Posts by merodev

<prev • 12 results • page 1 of 2 • next >
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LDplot using a matrix in R
... I have a matrix of LD values for different sites. ![examplematrix][1] https://ibb.co/eaURxQ I would like to get a LD plot like these: ![LDplot][2] https://ibb.co/cqAzHQ or ![LDplotbig][3] https://ibb.co/mqqYcQ I want the color shades to depict the numbers but the numbers do not need to be present. I ...
R gwas written 18 months ago by merodev140
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Answer: A: How to extract unique mapped results from Bowtie2 bam results?
... If you want only the uniquely mapped reads from bowtie2 sam files then you can proceed as follows: ``` grep -E "@|NM:" bt2output.sam | grep -v "XS:" > uniq_bt2output.sam ``` This first checks to see if there is alignment and then removes reads with secondary alignments. It will keep the header ...
written 2.8 years ago by merodev140
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Answer: A: Does Bowtie2 Preform Unique Mapping
... If you want only the uniquely mapped reads from bowtie2 sam files then you can proceed as follows: ``` grep -E "@|NM:" bt2output.sam | grep -v "XS:" > uniq_bt2output.sam ``` This first checks to see if there is alignment and then removes reads with secondary alignments. Hope this helps. ...
written 2.8 years ago by merodev140
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Comment: C: samtools mpeileup: extract SNPs between individuals only (discard SNPs betn indi
... Thanks Jorge! I followed this pipeline : ``` bowtie2 > samtools mpileup -uf ref.fa aln1.bam....aln100.bam -v > raw.vcf ``` Now I have all variants and then used ```bcftools call -mv raw.vcf>called.raw.vcf```. This file calls SNPs between my samples and the reference. Now I want to filter th ...
written 2.9 years ago by merodev140
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samtools mpeileup: extract SNPs between individuals only (discard SNPs betn individuals & reference)
... I used samtools after aligning Illumina reads from > 100 samples to a reference genome and used mpileup to call variants. Now, I want to discard the SNPs that compare an individual with the reference and keep the SNPs that are between the individuals only. Is there any ways to get this done? Than ...
samtools reference snp mpileup written 2.9 years ago by merodev140
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Answer: A: Merge three assembled files (iterations) into one.
... I haven't used stringtie. What you might want to do is merge all transcripts (from both wild and mutant) into a single file with cuffmerge. This gives you a full list of transcripts. You can then use cuffdiff to get the differentially expressed genes following the pipeline. ...
written 4.0 years ago by merodev140
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PBcR using less than 25X for error correction in PacBIo
... Hello everyone, When running PBcR for pacbio data, how do I select only the longest 15X coverage for assembly rather than the default 25X? Thanks, -Dave ...
pacbio pbcr error error-correction written 4.0 years ago by merodev140 • updated 3.9 years ago by orange30
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Answer: A: how to calculate the correlation and p values for all combination of a gene expr
... Have you tried LaF package to read your data? It works great with big sets of data as it does not load your data to RAM. cor then is quite fast to work on expression data.   ...
written 4.1 years ago by merodev140
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Pacbio: extract fastq from h5 file based on quality filtering
... Hi, I am new to pacbio and have 2 sets of .h5 files as output from pacbio. I am planning to use celera assembler and for that i need fastq files from .h5 files. 1) Is there any way to convert .h5 to fastq. 2) Is there any specific method to filter pacbio reads based on quality? 3) Do we combine b ...
assembly hgap long reads celera pacbio written 4.1 years ago by merodev140 • updated 2.4 years ago by mehmetgoktay19890
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Comment: C: Freebayes and snpeff give different number of SNPs
... Thank you Pablo. This was exactly what I was looking for! ...
written 4.2 years ago by merodev140

Latest awards to merodev

Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How to extract unique mapped results from Bowtie2 bam results?
Great Question 2.8 years ago, created a question with more than 5,000 views. For Pacbio: extract fastq from h5 file based on quality filtering
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Freebayes and snpeff give different number of SNPs
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Pacbio: extract fastq from h5 file based on quality filtering

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