Hello everyone,
I have to collect some metrics about a MiSeq run.
I used CASAVA for demultiplexing (namely the configureBclToFastq.pl...
15 results in 0.0028 seconds.
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Global metrics about a run
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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... -
Best way to realign / test other aligners with bams generated with casava
Hi
Long story short. Only got bams from casava (and misc other bams and files BUT no fastq) from seq provider ...
I actually wish to use... -
How to Demultiplex a Nextera paired-end MiSeq run
Has anybody been able to successfully demultiplexed a Nextera paired-end MiSeq run?
The current MiSeq Reporter cannot demultiplex and produce individual... -
automated pipeline casava or FASTQ script/program
Hi all,
is there any where I can find pointers/program/script to do automated casava or FASTQ file generation ...upon completion of a run?... -
IGV - Genome problems
Hello,
I want to use IGV to see my GAIIx data (CASAVA v1.8). I import my bam files(.bam and .bam.bai) in IGV. I have to use a different... -
What might cause the "Sequence Duplication Levels" failures in FastQC report?
Hello Everyone,
We are dealing with exome sequencing data of tumor samples.
After using FastQC to assess the quality of data,... -
Default Change in CASAVA / BCL->FASTQ
We are planning a minor release of CASAVA in October that is primarily intended to handle an improvement to the number of supported index sequences. ... -
CASAVA v1.8 with indels
My Settings :
Biology : GAIIx, SureSelect capture, paired-end 2x76 with "in house" indexing
BioInformatics : CASAVA... -
problem running runRNA.pl in CASAVA for RNA-seq data with multiple indexes
I have a RNA-seq dataset run in one lane from Illumina. Each sample has 3 indexes.
I have ran demultiplex.pl and Gerald.pl successful.... -
Demultiplexing and CASAVA 1.7
Hello,
I am looking for young bioinformatics. I need tools to perform demultiplexing
tool (script) to sequences from the GAIIx before... -
Upcoming changes in CASAVA
Hi everyone,
my name is Semyon and I work in Bioinformatics at Illumina. Our team has prepared a document describing the major changes... -
Installing CASAVA on OS X 10.6.5 Snow Leopard
I attempted to install Casava on OS X (10.6.5 Snow Leopard) and it didn't go so well out of the box. I was told it's not supported. I did a cursory search... -
Problem with CASAVA (GERALD) - Missing 'chromosome' element
Hi all,
I'm trying to run GERALD with eland_rna analysis and getting the following error:
ERROR: Missing 'chromosome' element... -
mRNA seq 75bp splice file
Illumina provides a human.49.splice ELAND_RNA_GENOME_SPLICE file for 50bp reads. Does someone have the same file for 75bp reads?
There...
