User: sun.nation

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sun.nation120
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Posts by sun.nation

<prev • 47 results • page 1 of 5 • next >
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Comment: C: convert GFF to GTF?
... Thanks I was able to figure out. ...
written 18 months ago by sun.nation120
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more than one annotation at a locus in SnpEff output?
... I created the genome database by myself and ran: $JAVA -jar /home/sshrest1/bin//snpEff/snpEff.jar Corynespora c1VSc2.vcf > c1VSc2_annotated.vcf I am getting multiple annotations at a locus. I was not able to figure out the issue, any thoughts? scaffold_1 3820284 . G A ...
snpeff written 18 months ago by sun.nation120 • updated 25 days ago by jilguero88810
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convert GFF to GTF?
... I am trying to convert gff to gtf. I got this from JGI. scaffold_1 JGI exon 6764 7298 . - . name "estExt_Genewise1.C_1_t10003"; transcriptId 510443 scaffold_1 JGI CDS 6997 7298 . - 2 name "estExt_Genewise1.C_1_t10003"; ...
gtf gff written 18 months ago by sun.nation120
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Comment: C: How to find % alignment of total reads to genic region?
... Thanks, second link worked: gff2bed < Corca1_all_genes_20140615.gff > Corca.bed cut -f1,2,3,8 Corca.bed > Corca-selected.bed egrep -v "stop_codon|start_codon" Corca-selected.bed > corca-final.bed bgzip corca-final.bed tabix corca-final.bed.gz bgzip after-snps_har ...
written 2.0 years ago by sun.nation120
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How to find % alignment of total reads to genic region?
... When we align reads to reference genome with gff annotation file, how can we know that ..% of total reads got aligned to annotated regions of the reference genome. Is there any tool to check this? ...
gff alignment bowtie written 2.0 years ago by sun.nation120 • updated 2.0 years ago by Jeffin Rockey660
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Comparative genome analysis of a species from different hosts?
... I had three Illumina whole genome of a single species. Two from cotton and one from soybean. There is a reference genome from JGI which was isolated from rubber. I did a strict alignment to this reference and called SNPs separately as well as mpileup with GATK. This is a haploid species so I filtere ...
snps genomics comparative written 2.0 years ago by sun.nation120
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GATK DP filter for multiple samples
... I used GATK to call SNPs and filter based on DP < 10. I did get SNPs but having problems to get filtered SNPs. Command to filter SNPs: $java -jar $gatk \ -T VariantFiltration \ -R Corca1_AssemblyScaffolds.fa \ -o snpsDPlt10.vcf \ --variant snps.vcf \ --gen ...
gatk snps written 2.0 years ago by sun.nation120
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Comment: C: vcftools DP filter error
... Using `--remove-filtered-geno-all` didn't help either. It gave the same output. ...
written 2.0 years ago by sun.nation120
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vcftools DP filter error
... I used this command: vcftools --vcf cotton2.all.bcf.vcf --out cotton2.all.bcf.vcf.maf1.vcf \ --remove-filtered-all --max-missing-count 0 --minDP 10 --minQ 10 \ --maxDP 1000 --maf 1.0 --recode --recode-INFO-all to filter SNPs with less than 10 reads but still got SNPs with < 10 DP. ...
vcftools written 2.1 years ago by sun.nation120 • updated 2.1 years ago by Brice Sarver2.4k
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Comment: C: Fastest way to search barcode string with two mismatches in fastq file using per
... Thanks, I will post complete code and downstream results as I go through ...
written 2.2 years ago by sun.nation120

Latest awards to sun.nation

Popular Question 17 months ago, created a question with more than 1,000 views. For paired end quality filtering
Popular Question 18 months ago, created a question with more than 1,000 views. For paired end quality filtering
Popular Question 23 months ago, created a question with more than 1,000 views. For paired end quality filtering
Popular Question 24 months ago, created a question with more than 1,000 views. For paired end quality filtering
Popular Question 2.2 years ago, created a question with more than 1,000 views. For vcf SNP file minor allele frequency filter?
Student 2.2 years ago, asked a question with at least 3 up-votes. For Fastest way to search barcode string with two mismatchs in fastq file using perl?

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