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Forum: Bioinformatics 10-31-2013, 10:16 AM
Replies: 5
Views: 2,981
Posted By agupta29
Can someone direct me to a source for the hg19,...

Can someone direct me to a source for the hg19, UCSC transcript annotation file. I generated one from the knownGene.txt file in iGenomes' hg19 package using genePredToGtf...
Forum: Bioinformatics 08-23-2013, 10:00 AM
Replies: 5
Views: 7,095
Posted By agupta29
Hi, Did you ever find an answer to this...

Hi,

Did you ever find an answer to this question? I am using both bwa-mem and bwa-aln to align human genome sequencing data and get similar errors using Picard ValidateSamFile.jar at the end.
...
Forum: Bioinformatics 08-09-2013, 11:24 AM
Replies: 10
Views: 4,599
Posted By agupta29
BWA and BWA mem I an using reverse-complemented...

BWA and BWA mem
I an using reverse-complemented reads. That brings the --rf orientation mate pair reads into --fr paired end orientation, which can then be used for bwa alignment. I am running...
Forum: Bioinformatics 08-09-2013, 10:33 AM
Replies: 10
Views: 4,599
Posted By agupta29
The libraries were prepared by Illumina Mate Pair...

The libraries were prepared by Illumina Mate Pair Library Preparation Kit v2 and sequenced using HiSeq2000 generating 2*100bp reads.

The alignments were done using bwa aln with default parameters....
Forum: Bioinformatics 08-09-2013, 08:44 AM
Replies: 10
Views: 4,599
Posted By agupta29
Mate pair sequencing - quality, duplication, throughput

We recently got Illumina mate pair sequencing data for a human sample. I am trying to do some some Quality Check to see how good the data is.

I used bwa for alignment and the output bam file...
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