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Forum: Bioinformatics 06-27-2018, 02:07 AM
Replies: 0
Views: 682
Posted By EHC
identify copies of long repeats

I have a question maybe someone can point me where to start looking for now it is still theoretical.
I have a yeast genome sequences by illumina paired end and I know a typical sequence of...
Forum: General 10-07-2011, 05:32 AM
Replies: 5
Views: 6,845
Posted By EHC
use paste

PASTE(1) BSD General Commands Manual PASTE(1)

paste -- merge corresponding or subsequent lines of files

paste [-s] [-d list] file ......
Forum: General 10-06-2011, 11:27 AM
Replies: 0
Views: 1,687
Posted By EHC
Dindel SAM/BAM format - viewing with IGV


I would like to get the SAM or BAM files of the events I got in the variantCalls.VCF final file. I use --processRealignedBA and then screen the bam files for the ones with the relevant...
Forum: Bioinformatics 06-23-2011, 07:37 AM
Replies: 1
Views: 2,301
Posted By EHC
Question dindel output

Hello All,

I run Dindel and now I am trying to understand the output. I did not find an example describing each column in the output.
Can someone please point me to the right place or help me...
Forum: Bioinformatics 05-25-2011, 01:26 PM
Replies: 3
Views: 1,733
Posted By EHC
Thank you Laura. I am interested in reads that do...

Thank you Laura. I am interested in reads that do not behave as expected (mainly broken reads). Is there any easy way to get these in a specific region.
Forum: Bioinformatics 05-23-2011, 08:40 AM
Replies: 3
Views: 1,733
Posted By EHC
1000 genomes - a beginner question


First, thank you for your time!

I work on yeast NGS. I like to run an analysis based on the 1000 genomes.
What kind of computer/facility I need?

I would like to be able to analyze...
Forum: Genomic Resequencing 07-29-2010, 01:01 PM
Replies: 0
Views: 2,467
Posted By EHC
pileup format- what is ^F


I am parsing the the read bases column of pileup format (bwa & samtools). Please help me to figure out how to get the base appear in the beginning of the read?

Forum: Bioinformatics 06-11-2010, 09:50 AM
Replies: 0
Views: 1,926
Posted By EHC
samtools rm ambiguous alignment


I am new here, glad I find this place.

Am I right that "samtools view -q 1" should remove all bwa will ambiguous alignments ? (since BWA ambiguous alignment should have MAPQ=0)

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