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Search: Posts Made By: wzhangvv
Forum: Bioinformatics 05-27-2013, 07:36 AM
Replies: 0
Views: 1,072
Posted By wzhangvv
Unhappy Ask for help! GATK iteration~

Hi,
I recently used several aligners to do the tests for SNPs calling. Without any iteration step, the bowtie2-local-very sensitive performed better than bwa. It could call more real SNPs than both...
Forum: Bioinformatics 11-19-2012, 07:29 AM
Replies: 1
Views: 872
Posted By wzhangvv
rate Ask for help! how to integrate BAC scaffolds and Illumina Data

Hi All,

This is my first time to do de novo genome assembly for a specific region. Now I have assembled BAC scaffolds and I also assembled illumina short reads to scaffolds using SGA assembler....
Forum: Bioinformatics 10-16-2012, 11:33 AM
Replies: 1
Views: 2,146
Posted By wzhangvv
Help! about Stacks populations command, VCF and sql files output

Hi all,
Recently I used populations with parameters -s -V to calculate Fst. And now I am stuck by 2 problems:
I got a VCF file but I can't find an index for it. I still can't build index by myself...
Forum: Bioinformatics 10-14-2012, 12:23 PM
Replies: 8
Views: 2,475
Posted By wzhangvv
Hi, This is the whole genome data and I don't...

Hi,
This is the whole genome data and I don't know the exact targeted regions...So I can't start with a known VCF file.
Thanks for your reply!
Forum: Bioinformatics 10-08-2012, 08:56 AM
Replies: 0
Views: 964
Posted By wzhangvv
Help! about Samtools mpileup output

Hi all,
I try to use Samtools to call SNPs. This is my first time to use mpileup. My output ALT column contains a bunch of "X". I really don't know what they mean. After I use bcftools with -bvcg...
Forum: Bioinformatics 10-05-2012, 02:07 PM
Replies: 3
Views: 2,550
Posted By wzhangvv
try add this parameter -XX:PermSize=8g...

try add this parameter -XX:PermSize=8g -XX:MaxPermSize=8g after -Xmx8g. It will assign more java heap space to picards
Forum: Bioinformatics 10-05-2012, 10:39 AM
Replies: 8
Views: 2,475
Posted By wzhangvv
Hi, Do you think there is anything wrong in my...

Hi,
Do you think there is anything wrong in my workflow? Can you give me some advice? I really don't know how to improve and debug it because the previous steps finished smoothly.:(
Really...
Forum: Bioinformatics 10-05-2012, 06:51 AM
Replies: 8
Views: 2,475
Posted By wzhangvv
Hi, Thanks for your reply! I just did de...

Hi,
Thanks for your reply!
I just did de novo assembly and got millions of contigs without any chromosome info...:( The frog species I worked on doesn't have an assembled genome...
I tried to...
Forum: Bioinformatics 10-04-2012, 08:23 PM
Replies: 8
Views: 2,475
Posted By wzhangvv
Hi, Thanks for your reply! I just read...

Hi,

Thanks for your reply!

I just read the menu of OpenGE. It can't help me because its localrealign step requires the intervals file which need to be generated by GATK RealignerTargetCreator,...
Forum: Bioinformatics 10-04-2012, 02:34 PM
Replies: 8
Views: 2,475
Posted By wzhangvv
Unhappy Help! about GATK realignment speed

Hi All,
I try to do SNP calling using GATK. This is my first time to do such things and I generated the work flow as follows. Everything went well till I was blocked by RealignerTargetCreator. It...
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