Hey guys,
I apologize for the possibly stupid question I will ask. The problem is that I met the error "java.lang.IllegalArgumentException:...
24 results in 0.0037 seconds.
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GATK Haplotype error with Novoalign
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Novoindex Bisulfite fastq options
I have paired end fastq files but I can't figure out which option my file falls under -b, -b2, or -b4. Has anyone had experience doing this and can clarify... -
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... -
Need to compare multiple mpileups for coverage overlap
I have 11 mpileups generated by novoalign from whole genome sequencing of Daphnia, which has a genome size of ~200MB. Each is the result of alignment... -
Novoalign inappropriately softclipping?
I have downloaded some exome data that appears to have been aligned using Novoalign
I determined this from the header:
@PG ID:novoalign... -
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... -
NovoalignCS syntax help
Hi,
I'm having lot of trouble giving the right syntax for NovoalignCS. I have paired reads of SOLiD data and want to map them to human... -
Novoalign miRNA error
I get the following error:
$./novoalign -d ./Homo_sapiens_GRCh37.ndx -f xyz.fastq -F ILM1.8 -m99 -l18 -rAll -c14 -o sam
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Novoalign with a lot of genomic data
For our usecase we intend to load Novoalign with the reference genomes for ALL Bacteria, Human, Viral, Fungi, Mouse, Honey Bee, Tazmanian Devil, Gorilla,... -
mapping quality score in tophat sam file
Hello all,
I have been trying to work with the sam output file that I received from tophat. My input file was an RNA-sequencing... -
Novoalign with softclipping OFF (-o FullNW)?
In the latest versions of novoalign, there is some softclipping for local alignment included by default. Supposedly this can be deactivated by using the... -
setting parameters for Novoalign 2-6 bp insertions deletions
I am looking for insertions 2-6 bp in length in the native novoalign output - but see that novoalign did not output any insertions greater than 1 bp.... -
Novoalign speed tips for 25bp reads
I'd like to use novoalign for alignments since I've found it to be very accurate, but it is very slow at short read lengths.
Heng li stated... -
Appropriate Reference Format
Hello,
I am trying to deal with some targeted resequencing data. I have a subset of hg19 that I targeted with a SureSelect Capture array... -
Can novoalign use FASTA as a reference format? (Specifically for mapping paired-end)
I am trying out novoalign to map paired-end reads from illumina data.
Here is the command line I am using:
...Code:
