Webinar on DNA-Seq data analysis- Case Studies
DNA-Seq data can be analyzed and visualized using an extensive workflow in Strand NGS software....
33 results in 0.0031 seconds.
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Webinar on DNA-Seq data analysis- Case studies
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Need suggestions to quantify genomic activity
Hello,
I'm trying to compare different strands of s.pombe, primarily in terms of genomic activity. What I mean by that is insertions, deletions,... -
Indels quantifications with MiSeq
Dear all,
I have troubles for analysing CRISPR experiments with sequencing. I am using PCR to amplify the target sequence of my sgRNA (classical... -
Problem with Pindel output
Hi,
I have been using normal/tumor GATK processed realigned and recalibrate bam files for mutation , indel and CNV analysis. I have used... -
Pindel Algorithm Explanation
Hey,
I am looking at the Kai Ye paper on Pindel:
http://bioinformatics.oxfordjournals...865.full.pdf+h... -
bwa mem and pindel
Dear all,
Thank you very much to all of you in advance for all the help I am sure I will receive. I am having problems running Pindel on bam files... -
BWA MEM and PINDEL
Dear all,
Thank you very much to all of you in advance for all the help I am sure I will receive. I am having problems running Pindel on bam files...Last edited by Ivarela; 06-25-2014, 09:20 AM. -
De novo assembly of reads
For de novo assembly of reads around the predicted insertion / deletion in VCF files.
1.) How many base pairs flanking the indels are... -
Validating Predictions of small insertions / deletions
Hi,
I have vcf files with indels which I created using GATK's Unified Genotyper.Is there any tool to vaildate those predictions?
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Death by Genomic Sudoku
I am a grad student with Promethean aspirations, and the challenges that come with such an undertaking.
I have 154 chromatograms of heterozygous... -
Getting insertion counts from DNA sequence data
For matched tumor and normal pairs, we easily get insertion and deletion counts from the output of Somatic Indel Detector in GATK. However, when we run... -
Tools for estimation of indels and refinement for multiple sequence alignments
Hi guys,
I have a multiple sequence alignment performed by MUSCLE program in fasta format.
I would like to use some tool to refine... -
varscan - filter out those snps close to indels
hi,
just a quick question about the somaticFilter provided by Varscan:
--indel-file File of indels for filtering nearby... -
snps & indels.txt CASAVA Illumina
Hi all,
I use the CASAVA pipeline with a GAIIx sequencer. Output, I get the BAM files and snps.txt and indels.txt. I try to convert these... -
Annotating indels
Hello,
I apologize for asking what may be a really silly basic question.
I identified cancer specific SNPs with GATK's...
