15 results in 0.0021 seconds.
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bowtie 2 dpad parameter explanation
Can someone provide a detailed explanation, what the bowtie2 parameter "--dpad" does? The explanation given in the manual is as follows: "--dpad... -
STAR Alignment parameters for varying complexity in library
I'm working with TruSeq data for the mouse genome, with one of the groups having a low complexity library, and the other two having a high complexity... -
Rapidr invalid class “SummarizedExperiment”
Hello everybody,
I am trying to set up a pipeline to aneuploidy prenatal diagnostic. In order to perform the analysis, I am using rapidR.... -
Mapping Chip-seq with BWA or Bowtie2?
Hi,
I am new to next generation sequencing analysis. So I need to map my 8 ChIP-seq samples(transcription factor) and I don't want to use galaxy.... -
HGAP Parameters in SMRT Analysis
Hello,
We just got SMRT Analysis installed in our lab and are trying to use HGAP for the first time. We have uploaded a SMRT cell into... -
Beginner. basic parameter for MIRA using 454 FLX data
Hi.
i am a beginner in the de novo assambly of genome and have a big question. I am sequence the bacteria using 454 FLX and need assembler... -
BWA & GATK parallel parameters.
Hi everybody,
I just want to know if there is some place where I can find technical documentation about how BWA & GATK... -
cuffdiff - the -c parameter
Hello,
I'm running cuffdiff for DE.
I'm running with -c parameter as 10. I'm gettig test OK, while the raw counts at that... -
bowtie advantages over tophat
Hi everybody,
I am working of RNA-Seq data and would like to map them using bowtie and/or tophat.
I know that tophat calls... -
Samtools.1 Parameter Q's
We are optimizing a custom pipeline that uses some of the functions from Samtools.1 and have a couple of questions about the parameters:
... -
BWA parameters for mRNA-seq aligning against mRNA refseq
Hello
I am sure similar questions were posted earlier but I could not find the definitive answer.
So the question is what... -
SAMtools mpileup -C and -q parameters
I am looking into parameters of mpileup, and have a few questions. I'll start with the -C parameter which is recommended to be set to 50 for bwa alignments.... -
bowtie -m option
Hi everybody,
maybe I misunderstood it completely, but what is the option -m good for?
If I am looking for differentially regulated... -
Recommended BWA parameters for SOLiD data ...
Hi there,
I am trying to map single-end 33 bp SOLiD data using bwa. I mapped the data using bowtie (-v2 -m1 --best --strata i.e. uniquely... -
Building indexes with bowtie-build
Hello, I am currently trying to align two closely related genomes from multiple sequence fasta files. I have a target genome which is made of 1168 sequences...
