I was using BBMap already for successful mapping of RNA-seq data (paired-end, Illumina) to a multi-FASTA transcriptome. Now I tried...
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Error when bbmapping RNA-seq data
Hello
I was using BBMap already for successful mapping of RNA-seq data (paired-end, Illumina) to a multi-FASTA transcriptome. Now I tried... -
Run Tadpole (BBtools) only on sub-sets of reads from input files
Hey there,
I have been using tadpole for error correction (and BBtools in general) and I am extremely happy with its results and performance.... -
Dedupe on Geneious Prime
Hello. I am currently running Dedupe, a part of the BBTools plug-in on Geneious Prime, to remove duplicate reads. I have read that Dedupe detects and... -
bbduk memory error
Hello everyone,
I've installed bbmap throw 'sudo apt-get install bbmap' and also by downloading the package, untaring it and adding the... -
heavily used bionformatics software without publications
Hi all
I am curious to know from the Bioinformatics/Genomics/CompBio research community about popular or heavily used software that are... -
Has anyone used BBTools package to remove contaminants
I would like to remove mitochondrial, chloroplast and rDNA contaminants from read data using BBTools - I was wondering if anyone has used BBTools to do... -
Calling BBMerge from Java program
Hi,
I have a handful of metatranscriptome sequences that I would like to merge using BBMerge, and I've sorted them together into bidimensional... -
bbmerge detects different adapters
Hello,
I have some bacterial genomes which were sequenced using the Nextera Flex library prep kit ( insert size ~350 bp) and MiSeq paired... -
calctruequality in bbmap
I'm trying to recalibrate Q scores of a NextSeq run using MiSeq contigs assembled with Tadpole. The commands I used to map the reads to the reference... -
bbtools: how to properly set up rqcfilter
Dear all,
I've recently obtained some PE RNA-seq data from JGI. They have been cleaned using the rqcfilter tool (v. 37.17). Since I would like... -
BBRepair quality score changes
After running BBRepair the log file states: "Changed from ASCII-33 to ASCII-64 on input quality 97 for base C while prescanning." It does this... -
MinHash Sketch - A Tool for Rapid Sequence Comparison
MinHash Sketch is a method of rapidly comparing large strings or sets. In genomics, you can use it like this:
1) Gather all the kmers...Last edited by Brian Bushnell; 02-03-2017, 08:53 AM. -
Hisat2: Differing amount of reads in mates
Hello all,
I am aligning paired-end reads using Hisat2. Unfortunately, some of the fastq files were corrupted in transfer. I was able to... -
BBmap can not produce sorted bam
I used BBmap to map RNAseq data with the command:
/home/bac/software/bbmap/bbmap.sh in1=CYP51C_2_1.fq.gz in2=CYP51C_2_2.fq.gz ref=genome.fasta... -
Introducing KmerCompressor, a tool for set operations on kmers
I'd like to introduce a new BBTool, KmerCompressor. This will take a dataset and reduce it to its set of constituent kmers, and print an optimally-condensed...Last edited by Brian Bushnell; 10-06-2015, 04:49 PM.
