User: apl00028

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apl0002870
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Posts by apl00028

<prev • 59 results • page 1 of 6 • next >
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Ho can I add a standard desviation to my diversity values?
... I am trying to add a standard desviation to the pi values obtained from SNPgenie ( https://github.com/chasewnelson/SNPGenie#output ) I checked that I can add a bootstrap value if I use the type of analysis WITHIN-GROUP ANALYSIS and BETWEEN-GROUP ANALYSIS but no for WITHIN-POOL ANALYSIS, this is the ...
snp written 4 weeks ago by apl0002870
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Answer: A: How to set up my vcf with a minimum depth?
... Finaly I got my aim using this function: bcftools view --types snps --include 'INFO/DP>=20' scaffold_filt_OD_PV009_q10_variant.vcf > scaffold_filt_OD_PV009_q10_variant_filtered.vcf ...
written 4 weeks ago by apl0002870 • updated 4 weeks ago by ATpoint21k
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Comment: C: How to set up my vcf with a minimum depth?
... I am trying it using this function of that link: vcftools --vcf scaffold_filt_OD_PV009_q10_variant.vcf --out output_prefix --min-meanDP 20 --recode --recode-INFO-all but I get SNP with lower depth of 20 and filter some SNP with a depth higher than 20. When I tried use this function: vcftools --vc ...
written 4 weeks ago by apl0002870
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How to set up my vcf with a minimum depth?
... I am trying to set up the minimum depth which samtools mpileup considers a polymorphism for RNAseq samples. For that I did this: I did an align with BWA: bwa mem scaffold_filt_PV014_bwa PV009_1_cmv3.fq_pairs_R1.fastq PV009_2_cmv3.fq_pairs_R2.fastq > scaffold_filt_OD_PV009.sam I change s ...
snp written 4 weeks ago by apl0002870
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Comment: C: How can I detect low frequent polymorphisms ?
... It has the SNPs that I expected, but if you give me an alternative way to get them whitout use R, I will be heard new ideas. ¡Gracias! ...
written 6 weeks ago by apl0002870
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Comment: C: How can I detect low frequent polymorphisms ?
... Well, I think I got the solution, If I used the tool bcftools view to see how is the distribution of polymorphims along the reference genome I can obtain a report where every SNP is recorded. bcftools view variants_Amaranthus_sp.bcf > varian ...
written 6 weeks ago by apl0002870
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Comment: C: How can I detect low frequent polymorphisms ?
... I called it Problem because it was a proof and I did that with an small sample size. With the aim to avoid bias in polymorphisms detection I did next steps: I built a phylogenetic tree of my samples using a reference sequence of each group of this virus (2 classic strains and 3 emergent strains) and ...
written 6 weeks ago by apl0002870
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How can I detect low frequent polymorphisms ?
... Hi everybody, I am trying to detect polymorphisms (and their proportions) to sanger sequences of the genes that codify for Watermelon Mosaic Virus Coat protein: I used: To make an aligment: bowtie2-build REFERENCIA.fas REFERENCIA_index To index my reference: ...
snp written 6 weeks ago by apl0002870
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Comment: C: How do I get a GFF file
... Please, could you answer to me? How can I get this file? ...
written 7 weeks ago by apl0002870
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Comment: C: Filtering VCF file
... I think that each project is different, so I suggest to you asses your data and according with them establish a criteria ...
written 7 weeks ago by apl0002870

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Scholar 3 months ago, created an answer that has been accepted. For C: I can not load a fasta file in Rstudio

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