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Search: Posts Made By: wzhang1001
Forum: Bioinformatics 08-23-2012, 06:44 PM
Replies: 2
Views: 10,460
Posted By wzhang1001
Truncated file error

Hello,

I tried to convert bam file to sam using samtools but got the error msg:
truncated file.
samtools view -h -o out.sam in.bam
[main_samview]truncated file

Any idea how to fix this?
...
Forum: Bioinformatics 08-23-2012, 06:35 PM
Replies: 1
Views: 11,687
Posted By wzhang1001
Truncated file error

Hello,

I tried to convert bam file to sam using samtools but got the error msg:
truncated file.
samtools view -h -o out.sam in.bam
[main_samview]truncated file

Any idea how to fix this?
...
Forum: Bioinformatics 07-25-2012, 10:27 AM
Replies: 0
Views: 897
Posted By wzhang1001
extract reads carrying non-reference allele

Hi All,

I have a BAM file and I need to extract reads to fastq file carrying ONLY non-reference alleles at a single based location.

Can anyone please advise how to do it?

thanks in advance!!
Forum: Bioinformatics 07-19-2012, 10:32 AM
Replies: 4
Views: 4,643
Posted By wzhang1001
Hi all, Thank youf or all your help!

Hi all,

Thank youf or all your help!
Forum: Bioinformatics 07-17-2012, 11:03 AM
Replies: 4
Views: 4,643
Posted By wzhang1001
Amplicon sequencing remove primer & adapters

Hi,

I have amplicon sequencing experiment with amplicon length between 45 ~124 bases. The sequencing length is 150, which completely covers the amplicon.

I wanted to remove the primers and...
Forum: Bioinformatics 07-06-2012, 08:48 AM
Replies: 0
Views: 1,299
Posted By wzhang1001
GATK for Complete Genomics Exome sequecning data

Hello.

I have BAM files from Complete Genomics whole exome sequencing platform. Does anyone know what is the best tool(s)/workflow for variant calling using complete genomics BAM files?

Thanks...
Forum: Bioinformatics 02-06-2012, 06:30 AM
Replies: 31
Views: 9,269
Posted By wzhang1001
Yes. I followed the instructions posted on...

Yes. I followed the instructions posted on tophat-fusion, and created top_dir and copied ensGene.txt,ensGtp.txt,mcl,refGene_sorted.txt under top_dir, and also created a blast_human directory that...
Forum: Bioinformatics 02-06-2012, 06:15 AM
Replies: 31
Views: 9,269
Posted By wzhang1001
tophat-fusion-post empty results

hello Xia687 & Mrfox,

I have the same problem, and have been puzzled for a while ...

I can run tophat-fusion without any problems. But when I tried tophat-fusion-post, I always got empty...
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