Hi all,
I am trying to map reads (Paired End) from a sample to a reference assembly that is somewhat divergenct (~3%). So I used the bam file...
18 results in 0.0066 seconds.
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SUBJECT: Stampy software error with PairSorter
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Unknown error with Stampy
Hi all,
I am trying to do some paired-end mapping to a genome with Stampy, and I get an error that I don't manage to find any information... -
Best Aligner for Duplicated Sequences
I'm looking around for some input from fellow SEQers. I'm experimenting with different aligners. I'm looking for an aligner that does a good job of correctly... -
Stampy - Mapping multiple individuals to genome
Stampy - Mapping multiple individuals to genome
Hi everybody,
I am very very new to this world, so apologize if the following questions...Last edited by vivi7; 03-18-2014, 12:39 AM. -
stampy hash table overfull
Hey, I'm new to bioinformatics and currently trying to build a hash table for a reference genome using stampy.
I have built the .stdix... -
stampy error: Mixed single- and paired-end input
Dear forum members,
I am mapping a couple of samples using stampy with bwa mapping. Most of the samples map fine, but in two cases I get... -
Aligning Illumina paired-end data with read length 250 bp
Hi All,
I am quite new in this forum and newbie bioinformatician. I have a very basic question to ask. I have illumina paired-end genomic... -
Mapping genomic reads to divergent exome
I have been trying to map genomic Illumina data to a divergent reference in order to get the sequence of exons in my sample. The idea is that although... -
Stampy/BAM alignment error
Hi all,
I've been trying to run Stampy 1.0.20 on a BAM file (produced by BWA) that has aligned some Illumina paired-end reads, but it is...Last edited by henry2304; 12-12-2012, 03:43 PM. -
Stampy help
I've recently run Stampy for the first time using this:
./stampy.py -t 12 -g xentro3 -h xentro3 -o /ichec/work/nglif015b/stampy-1.0.21/out... -
Errors in mapping cancer exome data
I am trying to map the reads from the ERP000703 study (http://www.ncbi.nlm.nih.gov/sra/ERX013480). I am using stampy to do the paired end mapping and... -
Slow Pileup After Switching to Stampy
I'm calling the pileup like this:
I used to use BWA to generate...Code:samtools pileup -f ref.fa aln_reads.bam -c > out.pileup
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problem about stampy
After i run command like this:
python stampy.py -g hg19 -h hg19 --solexa --bwaoptions="-q10 hg19.fa " -o quick.sam --bwatmpdir=./tmp... -
Stampy alignment
Hello all,
Does anybody have the experience of using stampy for alignment?
Based on stampy's document:
Fast:... -
Dindel giving error for every candidate indel
I'm running Dindel 1.01 on bam files produced by BWA and Stampy, looking for small indels. All the steps run to completion but every candidate indel encounters...
