I'm trying to trim/filter low quality reads from paired-end exome-seq data, using BBDuk.
I used the command:
```
for...
28 results in 0.0032 seconds.
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BBDuk quality filtering not producing expected result
Last edited by reliscu; 10-13-2021, 09:15 AM. -
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... -
bbsplit not using all reads in library
I have RNA-seq files which I am wanting to split based on mapping to reference sequences. I am using bbsplit to map to the sequences and output separate... -
bbduk and removing adapters of varying length
I am analyzing some published Tn-seq data. There appears to be residual transposon sequence in the reads, preventing alignment. Unfortunately, this sequence... -
Trimming stringency w/ excessive data
I'm in the process of assembling a 500Mb animal genome and have both Illumina and PacBio data to work with using a hybrid assembly approach. Generally...Last edited by adamrork; 12-12-2019, 08:49 PM. -
Extract reads from paired-end fastq based on specific adapters with bbduk
Hello everyone, I am using bbduk.sh (from bbmap toolkit) to extract reads from paired-end fastq files based on the presence of specific adapters in the... -
Comparing bbduk with fastp for quality and adapter trimming
Hi
Has anyone compared results and performance of bbduk vs fastp when it comes to adapter and quality trimming of fastq read files?... -
How does trimq work in BBDuk?
I have recently discovered BBTools and find it very intuitive use. However, as I am pretty new to processing raw sequence data, I haven't got my head... -
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... -
Extract Seq from Primers on BBDuK
Hello guys, a newbie in here.
I have reads from nanopore, converted fast5 files into fastq, what i am trying to do is extract the sequences... -
Looking for the sequence of a particular transcript from sequencing data
First, let me tell you that I'm very new to the field of NGS and not much familiar with the set of tools commonly used for NGS data processing. However,... -
bbduk useshortkmers - no documentation
I am following an Illumina recommended pipeline which includes the bbduk option "useshortkmers=t". This option is not referenced in the bbduk... -
BBduk for NexteraXT
I'm using BBduk 38.00 for adaptor trimming on NexteraXT libraries multiplexed with i5 and i7 indices and sequenced on an NextSeq500 2x150:
... -
BBDuk java error when filtering using entropy?
Hello,
I am having an issue with a java error when trying to use BBDuk to remove low entropy sequences from a fastq file. The libraries... -
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...
