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Forum: Bioinformatics 07-03-2016, 06:47 PM
Replies: 1
Views: 739
Posted By jdpr_100
Distinguish homozygous Reference with Missing genotype after merging multiple VCFs

The SNPs were called for each individual and multiple VCF files were combined. Is it a way to find out missing genotypes and checks if it is homozygous Reference or no-called site after merging...
Forum: Bioinformatics 05-20-2015, 05:28 AM
Replies: 2
Views: 1,181
Posted By jdpr_100
Can anybody help me with that?

Can anybody help me with that?
Forum: Bioinformatics 05-19-2015, 01:58 PM
Replies: 2
Views: 1,181
Posted By jdpr_100
How to extract partial CDS from contigs

Hello to all.
I have illumina data (exon capture sequencing) assembled into contigs. Assembled contigs contain both exon and intron regions. A lot of contigs only include partial exon regions...
Forum: Bioinformatics 09-30-2014, 06:40 AM
Replies: 1
Views: 4,432
Posted By jdpr_100
How to filter out SNPs with Minor allele frequency less than 5% in VCF file

Hello,
I would like to filter out SNPs with allele frequencies in VCF file from multi-sample variant calling.
I tried VCFtools with the following commands, but it doesn't work.


Here is the vcf...
Forum: Bioinformatics 08-28-2014, 09:59 AM
Replies: 3
Views: 3,253
Posted By jdpr_100
Thank you the reply. It is quite helpful.

Thank you the reply. It is quite helpful.
Forum: Bioinformatics 08-27-2014, 01:00 PM
Replies: 3
Views: 3,253
Posted By jdpr_100
We encountered a non-standard non-IUPAC base in the provided reference '88'

Hi,
Currently, I am working with bowtie2 and GATK to call SNPs on sugarcane. I am using Sbicolor_v2.1_255.fa, sorghum genome downloaded from phytozome, as reference.
java -Xms128m -jar...
Forum: Bioinformatics 08-13-2014, 01:42 PM
Replies: 0
Views: 1,145
Posted By jdpr_100
SNP call after bowtie 2 alignment

Hello,
I am new to this field and have couples of simple questions regarding SNP calling.

I used Bowie 2 to do the alignment for 10 libraries and call SNP with the following commands:
samtools...
Forum: Bioinformatics 07-09-2014, 10:53 AM
Replies: 7
Views: 2,179
Posted By jdpr_100
I really appreciate your suggestions.

I really appreciate your suggestions.
Forum: Bioinformatics 07-09-2014, 07:34 AM
Replies: 7
Views: 2,179
Posted By jdpr_100
Hi all, Thanks for your suggestions. For me, 12...

Hi all, Thanks for your suggestions.
For me, 12 samples are only pilot experiment. Totally, we have 300 samples. If I align each sample individually, that would be time consuming. I am trying to...
Forum: Bioinformatics 07-08-2014, 02:16 PM
Replies: 7
Views: 2,179
Posted By jdpr_100
Thank you. .bam is binary file. How can I grep...

Thank you. .bam is binary file. How can I grep the read names?
Forum: Bioinformatics 07-08-2014, 12:57 PM
Replies: 7
Views: 2,179
Posted By jdpr_100
How to seperate the reads from each individual in

Hi all,
Illumina reads from 12 different genotypes were aligned with reference genome and call SNPs. I combined all reads together before alignment. After variant calling by samtools mpileup, how...
Forum: Genomic Resequencing 06-25-2014, 06:16 PM
Replies: 5
Views: 2,410
Posted By jdpr_100
Hi Brian Bushnell, Thank you for your suggestion....

Hi Brian Bushnell, Thank you for your suggestion. In my case, reads length range from 50 to 100bp. Can bwa-mem handle 50-100bp reads?
Forum: Genomic Resequencing 06-25-2014, 07:29 AM
Replies: 5
Views: 2,410
Posted By jdpr_100
Compared to 71% in Bowtie2, only 44% reads can be...

Compared to 71% in Bowtie2, only 44% reads can be mapped to reference genome using BWA. I expect at least 60%. I am not sure whether the results are normal or not. Or, there something wrong with -n...
Forum: Genomic Resequencing 06-25-2014, 07:05 AM
Replies: 5
Views: 2,410
Posted By jdpr_100
Why BWA output didn't agree with bowtie2

I am working on the alignment between single-end read and reference genome using BWA and bowtie2. I got different results from BWA and bowtie. I couldn’t figure out what I am doing wrong.
bowtie2...
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