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Forum: Bioinformatics 01-06-2011, 05:23 AM
Replies: 0
Views: 2,715
Posted By jianfeng.mao
failed annotating the example vcf file in the installation folder of VCFtools

Dear SEQanswers,

I need your helps on fixing problems I faced when annotating the
example vcf file (annotate.txt) in the installation folder of
VCFtools. I have listed the commands I used and...
Forum: Bioinformatics 12-31-2010, 05:51 AM
Replies: 1
Views: 4,979
Posted By jianfeng.mao
failed when merging the example VCF files using VCFtools

Dear SEQanswers,

I am learning VCFtools by executing VCFtools commands on VCF files in Examples folder of the VCFtools installation path. Please help me to fix the three problems followed and give...
Forum: Genomic Resequencing 12-20-2010, 07:26 AM
Replies: 2
Views: 4,350
Posted By jianfeng.mao
The first step works for me, I checked the...

The first step works for me, I checked the "var.raw.bcf".

the commmand:
$ /ebio/abt6_projects/backup/solexa_tools/SAMtools/samtools-svn/bcftools/bcftools view var.raw.bcf

the output:...
Forum: Genomic Resequencing 12-20-2010, 07:19 AM
Replies: 2
Views: 4,350
Posted By jianfeng.mao
mpileup failed when using samtools.pl varFilter

I used the upper 1000 lines of my sam file to test the pileup process. My mpileup failed, at the second step when using samtools.pl varFilter.

Could you give any directions? I am very new on it....
Forum: Bioinformatics 12-18-2010, 02:03 AM
Replies: 0
Views: 2,892
Posted By jianfeng.mao
help on "truncated file", when converting sam to bam

When I convert my sam file to bam file, I got "truncated file" in prompt, and also "[sam_read1] reference '503821040998320619' is ecognized as '*'". It is no such problem, when I converted other sam...
Forum: Bioinformatics 12-17-2010, 05:56 AM
Replies: 2
Views: 5,362
Posted By jianfeng.mao
Thanks drio, It is now working in the...

Thanks drio,

It is now working in the server. I hope it works this time.
Forum: Bioinformatics 12-17-2010, 03:15 AM
Replies: 2
Views: 5,362
Posted By jianfeng.mao
how to convert sam to bam with EOF marker in header

I aligned short reads by an nonpublished aligner. Then I converted the
alignments to sam, then bam, and sote bam. It looks they worked for
me. But, when I intend to index and mpileup bam of...
Forum: Bioinformatics 12-17-2010, 01:48 AM
Replies: 3
Views: 6,947
Posted By jianfeng.mao
Thanks for the kind reply. I am now just re...

Thanks for the kind reply.

I am now just re do what I have done (sam -> bam conversion; bam sorting) using the updated version SAMtools-0.1.12. I guess maybe different samtools verison will affect...
Forum: Bioinformatics 12-17-2010, 01:24 AM
Replies: 3
Views: 6,947
Posted By jianfeng.mao
Mr. Erik from samtools mailinglist gave me reply...

Mr. Erik from samtools mailinglist gave me reply like that:
--------------------------------------------------------------------------------------
I'm guessing (really guessing) that in your sort...
Forum: Bioinformatics 12-16-2010, 11:44 PM
Replies: 3
Views: 6,947
Posted By jianfeng.mao
help me on reheader ".bam for indexing and mpileup

I aligned short reads by an nonpublished aligner. Then I converted the alignments to sam, then bam, and sote bam. They worked for me. Now, I intend to index bam, and then to mpileup bams of multiple...
Forum: Bioinformatics 12-12-2010, 11:21 PM
Replies: 0
Views: 1,423
Posted By jianfeng.mao
how to get SNPs matrix for population genetic ananlysis

Dear seqanswers,

I am new to genomics and bioinformatics. In my current study, we have
sequenced the genomes of tens of accessions of a plant, using Illumina
next generation sequencer. The short...
Forum: Bioinformatics 12-12-2010, 11:11 PM
Replies: 0
Views: 1,187
Posted By jianfeng.mao
a workflow of population genomic operations/analysis

Dear seqanswers,

I just move from classical population genetics to genomics/population
genomics. I need to set up my genomic handling platform and ability. I
have used R for statistics for 3...
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