Hello
This might be a stupid question, but I have just discovered tool called Breseq for microbial variant and SV analysis. The problem...
18 results in 0.0029 seconds.
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Can I use only one read from paired end reads for breseq analysis?
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Recommendation 150nt single-end vs 2x75nt paired-end
We are in the planning phase for an experiment that requires sequencing of a DNA pool of length about 140bp. It is crucial that the entire fragment is... -
Best practice for preprocessing the bam file for copy number estimation
Hi all,
There are known limitations involved in the copy number estimation from exome sequencing (Tumor/Normal).
For instance...Last edited by ty23991; 03-21-2016, 12:07 PM. -
Lost pairing info after bwa mem
Dear all,
Seems I'm missing something trivial, but cant figure out.
I've got exome seq pipeline. 2 fastq files with corresponding...Last edited by ArtemLada; 01-10-2016, 01:51 AM. -
DESeq2 paired data: "model is not full rank"
Dear all,
I have a question that is similar to others I've seen, but I am still not sure how to solve it.
Data is:
... -
edgeR for paired cases
Hi all,
I am using EdgeR for DE analysis. I would appreciate if somebody could help me check my experiment design.
I have... -
FLASH not pairing obvious reads
I've been trying to use FLASH to combine reads that should overlap in read 1 and 2 in a recent MiSeq 2x251 run, but it seems to be missing obvious overlaps.... -
truseq paired reads - what strandedness parameters in tophat?
In RNA-seq, paired ends, stranded, done with TrueSeq - what parameter in tophat should be applied to see strandedness properly?
fr-firststrand... -
Paired Reads Mapping Across Chromosomes
Hello all,
I have some Illumina HiSeq paired end whole genome human data that has 2 - 3% of paired end reads where the two ends are mapping... -
Paired end reverse orientation?
Hi,
I was given a lot of Illumina paired end reads. ~300bp inserts were used.
If I wanted to combine these into one long read where... -
Forward adapter at end of forward paired end read?
So I was given a metatranscriptome prepped with the Nugen Ovation RNAseq kit.
The metatranscriptome was sequenced on a HiSeq 2000 paired... -
Question about SGS computational analysis for Cancer Genomics
I am currently working on a project where we have cancer and normal patient samples, in which we developed a pipeline for variant calls for SNPs and Indels.... -
Can Cuffdiff treat paired-end and single-end reads at the same time?
Hi there,
I run cuffdiff with two paired-end reads samples and 2 single-end reads samples at the same time the other day(after running... -
Unpaired reads in paired data
I have a paired read dataset in sam format. However some of the reads are unpaired with #0 a the end of their names. The flags indicate these are all... -
how much DNA do I need for paired-end sequencing?
Hello everybody,
I am doing library prep for paired end BISULFITE seq on Illumina GAII. I am a little bit confused about the amount of DNA that...
